88 Sidney Street, Cambridge, Massachusetts 02139

NOTICE OF ANNUAL MEETING OF STOCKHOLDERS

TO BE HELD ON TUESDAY,THURSDAY, JUNE 21, 201620, 2024

Dear Stockholder:

You are cordially invited to our Annual Meeting of StockholdersStockholders. The meeting will be a virtual meeting held via the internet on Tuesday,Thursday, June 21, 2016,20, 2024, beginning at 9:00 a.m., Eastern Time, at our offices located at 88 Sidney Street, Cambridge, Massachusetts 02139,Time. The meeting will be held for the following purposes:

The foregoing itemsOur Annual Meeting will be a virtual meeting of business are more fully describedstockholders, which will be conducted exclusively via the internet at a virtual web conference. There will not be a physical meeting location, and stockholders will not be able to attend the Annual Meeting in person. This means that you can attend the attached proxy statement, which forms a partAnnual Meeting online, vote your shares during the online meeting and submit questions for consideration at the online meeting. Stockholders of this notice and is incorporated herein by reference. Our boardrecord as of directors has fixed the close of business on April 22, 2016 as the record date for the determination of stockholders2024 are entitled to notice of and to vote at the annual meeting or any adjournment or postponement thereof.

All stockholders as of the record date are cordially invitedmeeting. In order to attend the meeting.meeting online, vote your shares electronically during the meeting and submit questions, you must register in advance at www.proxydocs.com/AGIO prior to the deadline of June 18, 2024 at 5:00 p.m., Eastern Time. Upon completing your registration, you will receive further instructions via email, including your unique links that will allow you access to the meeting and will also permit you to submit questions. Please be sure to follow instructions found on your Notice of Internet Availability of Proxy Materials, proxy card and/or voting instruction form and subsequent instructions that will be delivered to you via email. We believe that hosting a “virtual meeting” will enable greater stockholder attendance and participation from any location around the world.

At Agios we are keenly focused on the contribution we can make to environmental sustainability. Instead of mailing a paper copy of our proxy materials to all of our stockholders, this year we are again providing access to our proxy materials over the internet under the U.S. Securities and Exchange Commission’s “notice and access” rules. As a result, we are mailing to our stockholders a Notice of Internet Availability of Proxy Materials (the “Notice”) instead of a paper copy of this Proxy Statement and our Annual Report for the fiscal year ended December 31, 2023 (the “2023 Annual Report”). We are mailing the Notice on or about April 26, 2024, and it contains instructions on how to access our proxy materials over the internet. The Notice also contains instructions on how each of our stockholders can receive a paper copy of our proxy materials, including this Proxy Statement, our 2023 Annual Report, and a form of proxy card. All stockholders who do not receive the Notice, including stockholders who have previously requested to receive paper copies of proxy materials, will receive a paper copy of the proxy materials by mail unless they have previously requested delivery of proxy materials electronically. We have chosen to employ this distribution process to conserve natural resources and reduce the costs of printing and distributing our proxy materials.

We encourage all stockholders to attend the Annual Meeting online. Whether or not you plan to attend the Annual Meeting online, we encourage you to read this Proxy Statement and submit your proxy or voting instructions as soon as possible by using the internet as described in the instructions included on your Notice, by calling the toll-free telephone number included in the Proxy Statement, or, if you received a paper copy of the proxy materials, by completing, signing, dating and returning your proxy card. Further information about how to register for the Annual Meeting, attend the Annual Meeting online, vote your shares and submit questions for consideration at the meeting is included in the accompanying Proxy Statement.

A complete list of registered stockholders will be available to stockholders of record for examination at www.proxydocs.com/AGIO during the 10-day period ending on the day before the Annual Meeting

Thank you for your ongoing support and continued interest in Agios Pharmaceuticals, Inc.

By Order of the Board of Directors,

David P. Schenkein, M.D.

President and Brian Goff

Chief Executive Officer

Cambridge, Massachusetts

April 27, 201626, 2024

Important Notice Regarding the Availability of Proxy Materials for the Annual Meeting of Stockholders to be Held on June 20, 2024: This Proxy Statement and our 2023 Annual Report to Stockholders are available at www.proxydocs.com/AGIO. These documents are also available to any stockholder who wishes to receive a paper copy by calling (866) 648-8133, visiting www.investorelections.com/AGIO or emailing paper@investorelections.com.

TABLE OF CONTENTS

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88 Sidney Street, Cambridge, Massachusetts 02139

PROXY STATEMENT FOR THE 20162024 ANNUAL MEETING OF STOCKHOLDERS

TO BE HELD ON TUESDAY,THURSDAY, JUNE 21, 201620, 2024

INFORMATION CONCERNING SOLICITATION AND VOTING

This proxy statementProxy Statement contains information about our 2016 annual meeting2024 Annual Meeting of stockholders,Stockholders, or the annual meeting.Annual Meeting. The Annual Meeting will be held on Thursday, June 20, 2024, beginning at 9:00 a.m. Eastern Time. The meeting will be a virtual meeting held via the internet. In order to attend the Annual Meeting online, you must register in advance at www.proxydocs.com/AGIO prior to the deadline of June 18, 2024 at 5:00 p.m., Eastern Time. Upon completing your registration, you will receive further instructions via email, including your unique links that will allow you access to the meeting. Please be sure to follow instructions found on Tuesday, June 21, 2016, beginning at 9:00 a.m. local time, atyour Notice of Internet Availability of Proxy Materials, proxy card and/or voting instruction form and subsequent instructions that will be delivered to you via email. There will not be a physical meeting location, and stockholders will not be able to attend the Annual Meeting in person.

Except where the context otherwise requires, references to “Agios Pharmaceuticals,” “Agios,” “the company,” “our company,” “we,” “us,” “our” and similar terms refer to Agios Pharmaceuticals, Inc. and its consolidated subsidiaries. References to our offices located at 88 Sidney Street, Cambridge, Massachusetts 02139. website are inactive textual references only and the contents of our website are not incorporated by reference into this Proxy Statement.

This proxy statementProxy Statement and the enclosed proxy card are being furnished in connection with the solicitation of proxies by our board of directors for use at the annual meetingAnnual Meeting and at any adjournment of that meeting. All proxies will be voted in accordance with the instructions they contain. If you do not specify your voting instructions on your proxy, ityour shares will be voted in accordance with the recommendations of our board of directors.

These We are making this Proxy Statement, the related proxy materials, together withcard and our annual report to stockholders for our 2015the fiscal year areended December 31, 2023, or the 2023 Annual Report, available to stockholders for the first being mailed to stockholderstime on or about April 27, 2016.26, 2024.

Important Notice Regarding the Availability of Proxy Materials for the Annual Meeting of Stockholders to be Held on June 21, 2016:

This proxy statement and our 2015 annual report are available electronically at www.proxyvote.com.

GENERAL INFORMATION ABOUT THE ANNUAL MEETING AND VOTING

Why did you send me this proxy statement?do I have access to these materials?

We senthave made these proxy materials available to you this proxy statement and the enclosed proxy card because our board of directors is soliciting your proxy to vote at the 2016 annual meetingAnnual Meeting to be held on Thursday, June 20, 2024 at 9:00 a.m., Eastern Time, including at any adjournments or postponements of stockholders. This proxy statement summarizes information related to your vote at the annual meeting. All stockholders who find it convenient to do soAs a holder of record of common stock as of the close of business on April 22, 2024, you are cordially invited to attend the annual meeting in person. However, you do not need to attend the meetingAnnual Meeting online and are requested to vote on the items of business described in this Proxy Statement. This Proxy Statement includes information that we are required to provide to you under the rules adopted by the U.S. Securities and Exchange Commission, or the SEC, and that is designed to assist you in voting your shares. Instead, you may simply complete, sign and return

Why did I receive a notice in the enclosed proxy card. Alternatively, you may submit your vote viamail regarding the internet availability of proxy materials instead of a full set of proxy materials?

Because we care about the sustainability of our environment, and in accordance with SEC rules, we have elected to provide access to our proxy materials, including this Proxy Statement and our 2023 Annual Report,

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over the internet. Accordingly, we have sent a Notice of Internet Availability of Proxy Materials, or telephone by following the instructions set forth on the enclosed proxy card.

We intendNotice, to begin mailing this proxy statement, the attached notice of annual meeting and the enclosed proxy card on or about April 27, 2016 to allour stockholders of record entitled to vote at the annual meeting.Annual Meeting with instructions for accessing the proxy materials. We mailed the Notice on or about April 26, 2024 to all stockholders entitled to vote at the Annual Meeting.

All stockholders entitled to vote at the Annual Meeting will have the ability to access the proxy materials by visiting the website referred to in the Notice, www.proxydocs.com/AGIO. This makes the proxy distribution process more efficient and less costly and helps conserve natural resources. The Notice also contains instructions to request to receive, free of charge, a printed set of the proxy materials. You may request the printed set of proxy materials over the internet at www.investorelections.com/AGIO, by emailing paper@investorelections.com, or by calling (866) 648-8133.

The Notice also identifies the date and time of the virtual Annual Meeting; instructions on how to attend the Annual Meeting online; the matters to be acted upon at the Annual Meeting and our board of directors’ recommendation with regard to each matter; and information on how to access and vote the form of proxy.

Can I vote my shares by filling out and returning the Notice?

No. The Notice identifies the items to be voted on at the Annual Meeting, but you cannot vote by marking the Notice and returning it. The Proxy Statement provides instructions on how to vote by proxy over the internet or by telephone, by requesting and returning a printed proxy card, or by voting online during the Annual Meeting.

What does it mean if I receive more than one Notice?

If you receive more than one Notice, your shares may be registered in more than one name or in different accounts. Please follow the voting instructions on the Notices to ensure that all of your shares are voted.

What is the purpose of the annual meeting?Annual Meeting?

At the annual meeting,Annual Meeting, stockholders will consider and vote on the following matters:

(3)

To hold an advisory vote on the frequency of future advisory votes on the compensation paid to our named executive officers.

Stockholders will also act on any other business that may properly come before the meeting, or any adjournment or postponement thereof.

Why is the 2024 Annual Meeting a virtual, online meeting?

Our 2024 Annual Meeting will be a virtual meeting of stockholders where stockholders will participate by accessing a website using the internet. There will not be a physical meeting location. We believe that hosting a virtual meeting facilitates greater stockholder attendance and participation by enabling stockholders to participate remotely from any location around the world. Our virtual meeting will be governed by our Rules of Conduct and

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Procedures which will be posted at www.proxydocs.com/AGIO in advance of the meeting. We have designed the virtual Annual Meeting to provide the same rights and opportunities to participate as stockholders have at an in-person meeting, including the right to vote and ask questions through the virtual meeting platform.

How do I virtually attend the Annual Meeting?

We will host the Annual Meeting live online via webcast. In order to attend the Annual Meeting online, you must register in advance at www.proxydocs.com/AGIO prior to the deadline of June 18, 2024 at 5:00 p.m., Eastern Time. Online registration for the Annual Meeting will begin on or around April 26, 2024, and you should allow ample time for online registration. Upon completing your registration, you will receive further instructions via email, including your unique links that will allow you access to the meeting. Please be sure to follow instructions found on your Notice, proxy card and/or voting instruction form and subsequent instructions that will be delivered to you via email.

The webcast of the Annual Meeting will start at 9:00 a.m., Eastern Time, on June 20, 2024. We will have technicians standing by and ready to assist you with any technical difficulties you may have accessing the virtual meeting at 9:00 a.m., Eastern Time on June 20, 2024. If you encounter any difficulties accessing the virtual meeting during registration or at the time of the virtual meeting, please contact technical support by following the instructions provided to you upon registration for the Annual Meeting.

Who can vote?

Only stockholders of record at the close of business on April 22, 2016,2024, the record date for the annual meeting,Annual Meeting, are entitled to vote at the annual meeting.Annual Meeting. On this record date, there were 37,906,42256,772,966 shares of our common stock outstanding. Common stock is our only class of stock outstanding.

How many votes do I have?

Each share of our common stock that you own as of the record date, April 22, 2016,2024, entitles you to one vote on each matter that is voted on.

Is my vote important?

Your vote is important no matter how many shares you own.Please take the time to vote. Take a moment to read the instructions, chosechoose the way to vote that is the easiest and most convenient for you and cast your vote as soon as possible.

How do I vote?

If you are the “record holder” of your shares, meaning that you own your shares in your own name and not through a bank, brokerage firm or other nominee, you may vote:

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annual meeting, for your mailed proxy to be valid and your19, 2024, we will vote to count. Your shares will be voted according to your instructions. If you return your proxy card but do not specify how you want your shares voted on any particular matter, they will be voted in accordance with the recommendations of our board of directors.as you direct.

If your shares are held in “street name,” meaning they are held for your account by a bank, brokerage firm, or other nominee, you may vote:

Can I change my vote?

If your shares are registered directly in your name, you may revoke your proxy and change your vote at any time before the annual meeting. To do so, you must doby following one of the following:below procedures:

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If your shares are held in “street name,” you may submit new voting instructions with a later date by contacting your bank, brokerage firm, or other nominee. You may also vote in person atonline during the annual meeting,Annual Meeting, which will have the effect of revoking any previously submitted voting instructions, if you obtain a broker’s proxy as described in the answer to the questioninstructions; see “How do I vote?” above.

Will my shares be voted if I do not return my proxy?

If your shares are registered directly in your name,your shares will not be voted if you do not vote over the internet, by telephone, by returning your proxyor by mail prior to the Annual Meeting or online while virtually attending the Annual Meeting. If you submit a proxy card without giving specific voting instructions on one or more matters listed in the Notice, your shares will be voted as recommended by ballotour board of directors on such matters, and as the proxyholders may determine in their discretion how to vote with respect to any other matters properly presented for a vote at the annual meeting.Annual Meeting.

If your shares are held in “street name,”your brokerage firm may, under certain circumstances, vote your shares if you do not return your voting instructions. Brokerage firms can vote customers’ unvoteduninstructed shares on routinediscretionary matters but they will not be allowed to vote your uninstructed shares with respect to certain non-routinenon-discretionary items. If you do not timely return voting instructions to your brokerage firm to vote your shares, your brokerage firm may, on routinediscretionary matters, either vote your shares or leave your shares unvoted.

Your brokerage firm cannot vote your uninstructed shares on any matter that is not considered routine.discretionary. Proposal 1, the election of four Class II directors, and Proposal 2, an advisory vote on the compensation paid to our named executive officers, and Proposal 3, an advisory vote to determine the frequency of future advisory votes on the compensation paid to our named executive officers, are not considered routinediscretionary matters. If you do not instruct your brokerage firm on how to vote with respect to these items, your brokerage firm may not vote with respect to these proposals and those votes will be counted as “broker non-votes.” “Broker non-votes” are shares that are held in “street name” by a bank or brokerage firm that indicates on its proxy that it does not have or did not exercise discretionary authority to vote on a particular matter. Proposal 4,3, the ratification of the appointment of PricewaterhouseCoopers LLP as our independent registered public accounting firm for the fiscal year ending December 31, 2024, is considered a routinediscretionary matter, and your brokerage firm will be able to vote on that item even if it does not receive instructions from you, so long as it holds your shares in its name. We encourage you to provide voting instructions to your brokerage firm or other nominee. This ensures that your shares will be voted at the annual meetingAnnual Meeting according to your instructions. You should receive directions from your brokerage firm or other nominee about how to submit your voting instructions.

How many shares must be represented to hold the annual meeting?Annual Meeting?

A majority of our shares of common stock outstanding at the record date must be present in personvirtually or represented by proxy to hold the annual meeting.Annual Meeting. This is called a quorum. For purposes of determining whether a quorum exists, we count as present any shares that are voted over the internet, by telephone, by completing and submitting a proxy by mail, or that are represented in personvirtually at the meeting.Annual Meeting. Further, for purposes of establishing a quorum, we will count as present shares that a stockholder holds even if the stockholder votes to abstain or only votes on one of the proposals. In addition, we will count as present shares held in “street name” by banks, brokerage firms or nominees who indicate on their proxies that they do not have authority to vote those shares on Proposals 1, 2 or 3.are “broker non-votes”. If a quorum is not present, we expect to adjourn the annual meetingAnnual Meeting until we obtain a quorum.

The presence at the annual meeting, in personAnnual Meeting, virtually or by proxy, of holders representing a majority of our outstanding common stock as of the record date, April 22, 2016,2024, or approximately 18,953,21228,386,484 shares, constitutes a quorum at the meeting and permits us to conduct the business of the meeting.

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What vote is required to approve each matter and how are votes counted?

Proposal 1 — Election of Directors

The threefour nominees for director to receive the highest number of votes FOR election will be elected as directors. This is called a plurality.Proposal 1 is not considered a routinediscretionary matter.Therefore, if your shares are held by your brokerage firm in “street name” and you do not timely provide voting instructions with respect to your shares, your brokerage firm cannot vote your shares on Proposal 1. Shares held in “street name” by banks, brokerage firms, or nominees who indicate on their proxies that they do not have authority to vote the shares on

Proposal 1Broker non-votes will not be counted as votes FOR or WITHHELD from any nominee. As a result, such “broker non-votes”broker non-votes will have no effect on the voting on Proposal 1. You may:

Votes that are withheld will not be included in the vote tally for the election of directors and will not affecthave no effect on the results of the vote.voting on Proposal 1.

Proposal 2 — Advisory Vote on the Compensation Paid to Named Executive Officers

To approve Proposal 2, holders of a majority of the votes cast on the matter must vote FOR the proposal.Proposal 2 is not considered a routinediscretionary matter.Shares which abstain and broker non-votes will not be counted as votes in favor of, or with respect to, these proposalsthis proposal and will also not be counted as votes cast. Accordingly, abstentions and broker non-votes will have no effect on the outcome of these proposals.this proposal. Proposal 2 is non-binding. Because this vote is advisory and not binding on us or our board of directors in any way, our board may decide that it is in our and our stockholders’ best interests to compensate our named executive officers in an amount or manner that differs from that which is approved by our stockholders.

Proposal 3 — Advisory Vote on the Frequency of Future Advisory Votes on the Compensation Paid to Named Executive Officers

The approval of one of the three frequency options under Proposal 3 requires a majority of the votes cast on the matter.Proposal 3 is not considered a routine matter. Shares which abstain and broker non-votes will not be counted as votes in favor of, or with respect to, these proposals and will also not be counted as votes cast. Accordingly, abstentions and broker non-votes will have no effect on the outcome of these proposals. With respect to this proposal, if none of the frequency options (one year, two years or three years) receive a majority vote, we will consider the frequency that receives the highest number of votes cast by stockholders to be the frequency that has been recommended by stockholders. Proposal 3 is non-binding. Because this vote is advisory and not binding on us or our board in any way, our board may decide that it is in our and our stockholders’ best interests to hold an advisory vote on executive compensation more or less frequently than the alternative approved by our stockholders.

Proposal 4 — Ratification of Appointment of Independent Registered Public Accounting Firm

To approve Proposal 4,3, holders of a majority of the votes cast on the matter must vote FOR the proposal.Proposal 43 is considered a routinediscretionary matter.If your shares are held by your brokerage firm in “street name” and you do not timely provide voting instructions with respect to your shares, your brokerage firm may vote your unvoteduninstructed shares on Proposal 4.3. If your brokerage firm exercises this discretionary authority, no broker non-votes are expected to occur in connection with Proposal 3. If you ABSTAIN from voting on Proposal 4,3, your shares will not be voted FOR or AGAINST the proposal and will also not be counted as votes cast or shares voting on the proposal. As a result, voting to ABSTAIN will have no effect on the outcome of Proposal 4.3.

Although stockholder approval of our audit committee’s appointment of Ernst & YoungPricewaterhouseCoopers LLP as our independent registered public accounting firm for the fiscal year endedending December 31, 20162024 is not required, we believe that it is advisable to give stockholders an opportunity to ratify this appointment. If this proposal is not approved at the annual meeting,Annual Meeting, our audit committee will reconsider its appointment of Ernst & YoungPricewaterhouseCoopers LLP as our independent registered public accounting firm for the year endedending December 31, 2016.

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How does the board of directors recommend that I vote on the proposals?

Our board of directors recommends that you vote:

Are there other matters to be voted on at the annual meeting?Annual Meeting?

We do not know of any matters that may come before the annual meetingAnnual Meeting other than the election of our board ofClass II directors, the approval, on an advisory basis, of the compensation of our named executive officers, the frequency of future advisory votes on the compensation paid to our named executive officers, and the ratification of the appointment of our independent registered public accounting firm. If any other matters are properly presented at the annual meeting,Annual Meeting, the persons named in the accompanying proxy intend to vote, or otherwise act, in accordance with their judgment on the matter.

Who will count the votes?

The votes will be counted, tabulated and certified by Broadridge Financial Solutions, Inc.Mediant, a BetaNXT business.

Will my vote be kept confidential?

Your vote will be kept confidential and we will not disclose your vote, unless (1) we are required to do so by law (including in connection with the pursuit or defense of a legal or administrative action or proceeding), or (2) there is a contested election for the board of directors. The inspector of election will forward any written comments that you make on the proxy card to management without providing your name, unless you expressly request disclosure on the proxy card.

How do I submit a question at the Annual Meeting?

If you wish to submit a question, on the day of the Annual Meeting, beginning at 8:00 a.m., Eastern Time on Thursday, June 20, 2024, you may log into the virtual meeting platform using the unique link provided to you via email following the completion of your registration at www.proxydocs.com/AGIO, and follow the instructions there. Our virtual meeting will be governed by our Rules of Conduct and Procedures, which will be posted at www.proxydocs.com/AGIO in advance of the meeting. The Rules of Conduct and Procedures will govern the ability of stockholders to ask questions during the meeting, including rules on permissible topics, and rules for how questions and comments will be recognized and disclosed to meeting participants. All questions asked in accordance with the Rules of Conduct and Procedures received from stockholders before or during the virtual Annual Meeting will be posted on our website at investor.agios.com as soon as practicable following the Annual Meeting.

How can I find out the results of the voting at the annual meeting?Annual Meeting?

Preliminary voting results will be announced at the annual meeting.Annual Meeting. Final voting results will be tallied by the inspector of election and published in a current report on Form 8-K to be filed with the Securities and Exchange Commission, or SEC within four business days after the annual meeting.Annual Meeting.

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How and when may I submit a stockholder proposal, including a stockholder nomination for director for the 20172025 annual meeting?meeting of stockholders?

Stockholders wishing to suggest a candidate for director should write to our corporate secretary. In order to give the nominating and corporate governance committee sufficient time to evaluate a recommended candidate and/or include the candidate in our proxy statement for the 20172025 annual meeting of stockholders, the recommendation should be

received by our corporate secretary at our principal executive offices in accordance with our procedures detailed in the section below entitled “Stockholder Proposals.” Such submissions must state the nominee’s name, together with appropriate biographical information and background materials, and information with respect to the stockholder or group of stockholders making the recommendation, including the number of shares of common stock owned by such stockholder or group of stockholders, as well as other information required by our bylaws or SEC regulations. We may require any proposed nominee to furnish such other information as we may reasonably require in determining the eligibility of such proposed nominee to serve as an independent director or that could be material to a reasonable stockholder’s understanding of the independence, or lack thereof, of such proposed nominee.

Who is paying the costs of soliciting these proxies?

We will pay all of the costs of soliciting proxies. Our directors, officers and other employees may solicit proxies in person or by mail, telephone, fax or email. We will pay our directors, officers and other employees no additional compensation for these services. We will ask banks, brokerage firms and other nominees to forward these proxy materials to their principals and to obtain authority to execute proxies. We may reimburse them for their expenses.

How do I obtain an Annual Report on Form 10-K?

If you would like a copy of our Annual Report on Form 10-K for the year ended December 31, 20152023 that we filed with the SEC, we will send you one, without exhibits, free of charge. Please contact Renee Leck, Investor Relations. She may be contactedRelations at 88 Sidney Street, Cambridge, Massachusetts 02139; telephone: 617-649-8600;e-mail: renee.leck@agios.com. IR@agios.com.

All of our SEC filings are also available free of charge in the “Investors & Media — “Investors—Financials—SEC Filings” section of our website at www.agios.com.www.agios.com.

Whom should I contact if I have any questions?

If you have any questions about the annual meetingAnnual Meeting or your ownership of our common stock, please contact Renee Leck in our Investor Relations department. She may be contacted at 88 Sidney Street, Cambridge, Massachusetts 02139; telephone: 617-649-8600;e-mail: renee.leck@agios.com.

Cautionary Note Regarding Forward-Looking Statements

This proxy statement contains forward-looking statements within the meaning of The Private Securities Litigation Reform Act of 1995. Such forward-looking statements include those regarding the potential benefits of PYRUKYND^® (mitapivat); the company’s plans, strategies and expectations for its preclinical, clinical and commercial advancement of its drug development, including PYRUKYND^®; and the potential benefits of the Company’s strategic plans and focus. The words “aim,” “anticipate,” “believe,” “could,” “expect,” “goal,” “hope,” “intend,” “may”, “might,” “milestone,” “plan,” “potential,” “possible,” “strategy,” “will,” “vision,” and similar expressions are intended to identify forward-looking statements, although not all forward-looking statements contain these identifying words. Such statements are subject to numerous important factors, risks and

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STOCKHOLDERS SHARING THE SAME ADDRESS

The SEC has adopted rules promulgated by the SECthat permit companies banks, brokerage firmsand intermediaries (e.g., brokers) to satisfy the delivery requirements for Notices and, if applicable, our annual report and other proxy materials, with respect to two or other intermediariesmore stockholders sharing the same address by delivering a single Notice and, if applicable, a single set of our annual report and proxy materials, addressed to deliverthose stockholders. This practice, which is commonly referred to as “householding,” potentially means extra convenience for stockholders and cost savings for companies.

This year, a number of brokers with account holders who are our stockholders will be “householding” our proxy materials. A single Notice and, if applicable, a single copy of a proxy statement andour annual report and our proxy materials, will be delivered to households at which two or moremultiple stockholders reside. This practice, known as “householding,” is designed to reduce duplicate mailings and save significant printing and postage costs as well as natural resources. Stockholders sharing an address whounless contrary instructions have been previouslyreceived from the affected stockholders. Once you have received notice from your broker that they will be “householding” communications to your address, “householding” will continue until you are notified by their bank, brokerage firmotherwise or other intermediaryuntil you revoke your consent.

If, at any time, you no longer wish to participate in “householding” and have consentedwould prefer to householding will receive only one copya separate Notice and, if applicable, a separate set of our annual report and proxy statement and annual report.materials in the future, please notify your broker or contact us. If you wish to receive a separate set of our annual report and proxy materials for this year’s Annual Meeting, we will deliver them promptly upon written or oral request. Stockholders who currently receive multiple copies of the Notice, and, if applicable, our annual report and other proxy materials at their addresses and would like to opt outrequest “householding” of this practice for future mailings and receive separate proxy statements and annual reports for each stockholder sharing the same address, pleasetheir communications should contact your bank, brokerage firmtheir brokers or other intermediary from whom you received such mailing. We will promptly deliver a separate copy of the proxy statement and/or annual report to you if youus. To contact us, at the following addressdirect your written or telephone number:oral request to: Agios Pharmaceuticals, Inc., 88 Sidney Street, Cambridge, MA 02139, Attention: Corporate Secretary, 617-649-8600. Stockholders sharing an address that are receiving multiple copies of the proxy statement617-649-8600 or annual report can request delivery of a single copy of the proxy statement or annual report by contacting their bank, brokerage firm or other intermediary or by contacting uscontact Investor Relations at the address or telephone number above.

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SECURITY OWNERSHIP OF CERTAIN BENEFICIAL OWNERS AND MANAGEMENT

The following table sets forth information relating to the beneficial ownership of our common stock as of March 31, 2016,2024, by:

The percentage of shares beneficially owned is computed on the basis of 37,899,24056,751,112 shares of our common stock outstanding as of March 31, 2016.2024. The number of shares beneficially owned by each stockholder is determined under rules of the Securities and Exchange Commission.SEC. Under these rules, beneficial ownership includes any shares as to which the individual or entity has sole or shared voting power or investment power. In computing the number of shares beneficially owned by an individual or entity and the percentage ownership of that person, shares of common stock subject to options or other rights held by such person that are currently exercisable or will become exercisable within 60 days of March 31, 20162024 are considered outstanding, although these shares are not considered outstanding for purposes of computing the percentage ownership of any other person. Unless otherwise indicated, the address of all listed stockholders is c/o Agios Pharmaceuticals, Inc., 88 Sidney Street, Cambridge, MA 02139. Each of the stockholders listed has sole voting and investment power with respect to the shares beneficially owned by the stockholder unless noted otherwise, subject to community property laws where applicable.

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Flagship common stock. The Master Fund Flagship GP, and Dr. Afeyan and Mr. Kania (the “Reporting Persons”) expresslyspecifically disclaims beneficial ownership of the Shares except to the extentsecurities directly held by it by virtue of its inability to vote or his pecuniary interest therein.dispose of such securities as a result of its Investment Management Agreement with Armistice Capital. The principal business address for each of the Reporting PersonsArmistice Capital is One Memorial Drive,510 Madison Avenue, 7th Floor, Cambridge, MA 02142.New York, NY 10022.

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SECTION 16(a) BENEFICIAL OWNERSHIP REPORTING COMPLIANCE

Under Section 16(a) of the Exchange Act, directors, executive officers and beneficial owners of 10% or more of our common stock, or reporting persons, are required to report to the SEC on a timely basis the initiation of their status as a reporting person and any changes with respect to their beneficial ownership of our common stock. Based solely on our review of copies of such forms that we have received, or written representations from reporting persons, we believe that during the fiscal year ended December 31, 2015, all executive officers, directors and greater than 10% stockholders complied with all applicable filing requirements, except with respect to (i) a Form 4 filing made on October 30, 2015 to report shares of common stock sold by Dr. Schenkein on October 27, 2015, (ii) a Form 4 filing made on July 8, 2015 to report shares of common stock sold by Dr. Biller on April 8, 2015 and May 7, 2015, (iii) a Form 4 filing made on October 27, 2015 to report shares of common stock sold by Dr. Cantley on October 22, 2015 and October 23, 2015, and (iv) a Form 4 filing made on June 26, 2015 to report an option grant made to Dr. Ho on June 23, 2015.

PROPOSAL 1:

ELECTION OF DIRECTORS

Our board of directors is divided into three classes, with one class of our directors standing for election each year. Directors in each class are elected at the annual meeting of stockholders held in the year in which the term for their class expires and hold office for a three-year term and until their resignation or removal or their successors are duly elected and qualified. In accordance with our certificate of incorporation and bylaws, our directors may fill existing vacancies on the board of directors.

The term of office of our Class IIIII directors, Drs. David P. SchenkeinKaye Foster, Maykin Ho, Ph.D., Jeffrey Capello and Marc Tessier-Lavigne and Mr. Robert T. Nelsen,Catherine Owen will expire at the 2016 annual meeting.Annual Meeting. The nominees for Class IIIII directors for election at the 2016 annual meetingAnnual Meeting are Drs. SchenkeinMs. Foster, Dr. Ho, Mr. Capello and Tessier-Lavigne and Mr. Nelsen.Ms. Owen. If any of Drs. SchenkeinMs. Foster, Dr. Ho, Mr. Capello or Tessier-Lavigne or Mr. Nelsen areMs. Owen is elected at the 2016 annual meeting,Annual Meeting, such individual will be elected to serve for a three-year term that will expire at our 20192027 annual meeting of stockholders and until such individual’s successor is elected and qualified. Mr. Capello and Ms. Owen were elected to our board of directors effective in June 2023 by our board of directors, upon the recommendation of the nominating and corporate governance committee, and they are standing for election by our stockholders for the first time at this Annual Meeting.

If no contrary indication is made, proxies in the accompanying form will be voted for Drs. SchenkeinMs. Foster, Dr. Ho, Mr. Capello and Tessier-Lavigne and Mr. NelsenMs. Owen or, in the event that any of Drs. Schenkein or Tessier-Lavigne orMs. Foster, Dr. Ho, Mr. Nelsen areCapello and Ms. Owen is not a candidate or areis unable to serve as a director at the time of the election (which is not currently expected), for any nominee who is designated by our board of directors to fill the vacancy.

Our priority in selection of board members is identification of members who will further the interests of our stockholders through their established record of professional accomplishment, the ability to contribute positively to the collaborative culture among board members, knowledge of our business, understanding of the competitive landscape and adherence to high ethical standards. Certain individual qualifications and skills of our directors that contribute to the board of directors’ effectiveness as a whole are described in the following paragraphs.

Information Regarding Directors

The following paragraphs provide information as of the date of this proxy statementProxy Statement about each director and nominee for director, as furnished to us by the directors and nominees for director. The information presented includes information each such individual has given us about his or her age, all positions he or she holds, his or her principal occupation and business experience for the past five years, and the names of other publicly-held companies of which he or she currently serves as a director or has served as a director during the past five years. In addition to the information presented below regarding each such individual’s specific experience, qualifications, attributes and skills that led our board of directors to the conclusion that he or she should serve as a director, we also believe that each of our directors and director nominees has a reputation for integrity, honesty and adherence to high ethical standards. Each has demonstrated business acumen and an ability to exercise sound judgment, as well as a commitment of service to our company and our board.board of directors. Finally, we value their significant experience on other public company boards of directors and board committees.

Information about the number of shares of common stock beneficially owned by each of our directors and nominees for director appears above under the heading “Security Ownership of Certain Beneficial Owners and Management.”

There are no family relationships between or among any of our executive officers, directors or nominees for director.

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Nominees for Election to the Board of Directors

Term Expiring at the 20192027 Annual Meeting of Stockholders, if elected at the Annual Meeting (Class III)II)

David P. Schenkein, M.D. joined Agios in August 2009 as president, chief executive officer and a member of our board of directors. Dr. Schenkein has been a hematologist and medical oncologist for more than 20 years. He currently serves as an adjunct attending physician in hematology at Tufts Medical Center. Prior to joining Agios, from March 2006 to July 2009, Dr. Schenkein was the senior vice president, clinical hematology/oncology at Genentech, Inc., a pharmaceutical company (now a member of the Roche Group, a global healthcare company), where he was responsible for numerous successful oncology drug approvals and leading the medical and scientific strategies for its BioOncology portfolio. While at Genentech, he served as an adjunct clinical professor of medical oncology at Stanford University School of Medicine. Prior to joining Genentech, he served as the senior vice president of clinical research at Millennium Pharmaceuticals, Inc. (a wholly-owned subsidiary of Takeda Pharmaceuticals Company Limited), a biopharmaceutical company, overseeing the clinical development and worldwide approval of VELCADE^®, a first-in-class cancer therapy now approved to treat multiple myeloma and non-Hodgkins lymphoma. Dr. Schenkein currently serves on the board of directors of Foundation Medicine, Inc. and bluebird bio, Inc., both public biotechnology companies, and of Denali Therapeutics Inc., a private biotechnology company. Dr. Schenkein holds a B.A. in chemistry from Wesleyan University and an M.D. from the State University of New York Upstate Medical School. We believe that Dr. Schenkein’s detailed knowledge of our company and his extensive background in the biotechnology industry, including his roles at Genentech and Millennium, provide a critical contribution to our board of directors.

Robert T. Nelsen has served as a member of our board of directors since December 2007. Mr. Nelsen was a co-founder of ARCH Venture Partners, a venture capital firm, and has served in various capacities for ARCH and affiliated entities since July 1986. Mr. Nelson is currently a managing director of ARCH Venture Corporation. Mr. Nelsen has played a significant role in the early sourcing, financing and development of more than 30 companies. Mr. Nelsen is a director of Sapphire Energy, Inc., Ensemble Therapeutics Corporation, Juno Therapeutics, Inc., Syros Pharmaceuticals Inc., NextCODE Health (a subsidiary of WuXi PharmaTech Inc.), Hua Medicine Ltd., Saga Investments, LLC, Arivale Inc., Denali Therapeutics, Faraday Pharmaceuticals, Inc., GRAIL Bio (a subsidiary of Illumina, Inc.), Omniome, Sienna Biopharmaceuticals, Inc. and UNITY Biotechnology, Inc. Mr. Nelsen previously served as a Trustee of the Fred Hutchinson Cancer Research Institute, the Institute for Systems Biology, and as a director of the National Venture Capital Association. Mr. Nelsen previously served on the boards of Bellerophon Therapeutics, Inc., Fate Therapeutics, Inc., Elixir Pharmaceuticals, Inc., Ikaria Inc., Kythera Biopharmaceuticals, Inc., NeurogesX, Inc., Sage Therapeutics, Inc., and entities affiliated with deCode Genetics, Inc., among others. Mr. Nelsen received a B.S. with majors in biology and economics from the University of Puget Sound and an M.B.A. from the University of Chicago. We believe Mr. Nelsen is qualified to sit on our board of directors due to his extensive experience as an investor in, and director of, early stage biopharmaceutical and life sciences companies.

Marc Tessier-Lavigne, Ph.D. has served as a member of our board of directors since September 2011, including as chairman of our board of directors since June 2015. Dr. Tessier-Lavigne has served as president of the Rockefeller University, as well as professor and Head of the Laboratory of Brain Development and Repair, since March 2011. Previously, he was employed at Genentech from 2003 to March 2011, where he became executive vice president for research and chief scientific officer, and directed 1,400 people in disease research and drug discovery in cancer, immune disorders, infectious diseases and neurodegenerative diseases. Prior to his tenure at Genentech, Dr. Tessier-Lavigne was an investigator with the Howard Hughes Medical Institute from

1994 to 2003 and a professor at Stanford University and the University of California, San Francisco from 1991 to 2003. He is a member of the board of directors of publicly-traded biopharmaceutical companies Regeneron Pharmaceuticals Inc. and Juno Therapeutics and chairman of the board of Denali Therapeutics. He also serves on the board of trustees of the Rockefeller University and the Rockefeller Archive Center and the board of directors of the Federal Reserve Bank of New York. Dr. Tessier-Lavigne previously served on the board of directors of Pfizer Inc., a publicly-traded pharmaceuticals company. He is a member of the National Academy of Sciences and its Institute of Medicine, and a fellow of the Royal Society (UK), the Royal Society of Canada, the American Academy of Arts and Sciences, the American Association for the Advancement of Science, and the Academy of Medical Sciences (UK). Dr. Tessier-Lavigne earned undergraduate degrees from McGill University and from Oxford University, where he was a Rhodes Scholar. He received his Ph.D. from University College London, and conducted postdoctoral work at the MRC Developmental Neurobiology Unit in London and at Columbia University. Dr. Tessier-Lavigne’s qualifications to sit on our board of directors include his pioneering research, his deep scientific knowledge and his reputation as an exceptional leader in the biotechnology industry.

Recommendation of the Board of Directors

OUR BOARD OF DIRECTORS UNANIMOUSLY RECOMMENDS THAT THE STOCKHOLDERS VOTE FOR THE ELECTION OF DRS. DAVID P. SCHENKEIN AND MARC TESSIER-LAVIGNE AND MR. ROBERT T. NELSEN.

Members of the Board of Directors Continuing in Office

Term Expiring at the 2017 Annual Meeting of Stockholders (Class I)

Lewis C. Cantley, Ph.D. has served as a member of our board of directors since August 2007. Dr. Cantley has served as a director of the Cancer Center at Weill Cornell Medical College and New York-Presbyterian Hospital since October 2012. Prior to that, from 1992 to 2012, Dr. Cantley was a professor of systems biology at Harvard Medical School and chief of the division of Signal Transduction at Beth Israel Deaconess Medical Center, a major teaching hospital of Harvard Medical School in Boston. From 2007 to 2012, Dr. Cantley also served as director of the Cancer Center at Beth Israel Deaconess Medical Center. Dr. Cantley is a member of the American Academy of Arts and Sciences and the National Academy of Sciences, and serves on the editorial boards of the journalsCell and theJournal of Cell Biology. He currently serves on the board of directors of the American Association of Cancer Research and Hope Foundation for Cancer Research, non-profit organizations that promote cancer research. Dr. Cantley is the recipient of the 2005 Pezcoller Foundation-American Association for Cancer Research International Award for Cancer Research, for his leadership in the field of signal transduction, including the discovery of the phosphatidylinositol-3-kinase (PI3K) signaling pathway. Dr. Cantley received his B.S. in chemistry from West Virginia Wesleyan College, and obtained a Ph.D. in biophysical chemistry from Cornell University. Dr. Cantley’s qualifications to sit on our board of directors include his position as a foremost expert in understanding the biochemical pathways linking cancer and metabolism.

Paul J. Clancy has served as a member of our board of directors since September 2013. Mr. Clancy has more than 20 years of experience in financial management and strategic business planning, and has served as the executive vice president and chief financial officer at Biogen Inc. (formerly Biogen Idec), a publicly-traded biopharmaceutical company, since August 2007. He also served as senior vice president of finance of Biogen Idec, with responsibilities for leading the treasury, tax, investor relations and business planning groups. Prior to

the merger of Biogen and Idec, Mr. Clancy was the vice president of portfolio management at Biogen Inc. He joined Biogen Inc. in 2001 as vice president of U.S. marketing. Before Biogen Inc., Mr. Clancy spent 13 years at PepsiCo Inc., a publicly-traded food and beverage company, serving in a variety of financial and general management positions, including vice president and general manager of their Great West Business Unit. Mr. Clancy is a member of the Board of Directors of Incyte Corporation. Mr. Clancy has an MBA from Columbia Business School in New York City and received his B.S. in business administration from Babson College in Wellesley, MA. We believe Mr. Clancy is qualified to serve as a member of our board of directors due to his extensive financial and executive leadership experience at large multi-national companies.

Term Expiring at the

2018 Annual Meeting of Stockholders (Class II)

Douglas G. Cole, M.D. has served as a member of our board of directors since December 2007. Dr. Cole has been a general partner of Flagship Ventures, where he has focused on life science investments, since 2001. He currently serves on the board of directors of Editas Medicine, Inc., a public biotechnology company, and on the boards of directors of several private biopharmaceutical companies, including Denali Therapeutics, Ensemble Therapeutics, KSQ Therapeutics, Inc., Quanterix Corporation, Permeon Biologics, Inc., and Torque Therapeutics, Inc. In the past five years, Dr. Cole has served on the boards of Seventh Sense Biosystems, Inc., Resolvyx Pharmaceuticals, Inc., Receptos, Inc., AVEO Pharmaceuticals, Inc., Tetraphase Pharmaceuticals, Inc., Concert Pharmaceuticals, Inc., Selecta Biosciences, Inc., Avedro, Inc., Zalicus, Inc. (formerly CombinatoRx), Moderna Therapeutics, CGI Pharmaceuticals, Syros Pharmaceuticals and Morphotek Inc. Dr. Cole holds a B.A. in English from Dartmouth College and an M.D. from the University of Pennsylvania School of Medicine. We believe Dr. Cole’s qualifications to sit on our board of directors include his substantial experience as an investor in emerging biopharmaceutical and life sciences companies, as well as his experience serving on the board of directors for several biopharmaceutical companies.

Kaye Fosterhas served as a member of our board of directors since December 2014. Ms. Foster has more than 2528 years of experience in human resources in the pharmaceutical industry and ishas been a Senior Advisor at the former senior vice president, global human resourcesBoston Consulting Group since 2014 and in January 2022 joined ARCH Venture Partners as a venture partner. Previously, she was Senior Vice President, Global Human Resources at Onyx Pharmaceuticals, Inc., an Amgen, Inc., or Amgen, subsidiary and a biopharmaceutical company.company, or Onyx, from 2010 to 2014. At Onyx, which was acquired by Amgen in 2013, she led all aspects of human resources for U.S. and global operations. Prior to joining Onyx, Ms. Foster was global vice presidentGlobal Vice President of human resourcesHuman Resources and an executive committeeExecutive Committee member at Johnson and Johnson Corporation, a publicly-tradedpublicly traded healthcare company, from 2003 to 2010. Before Johnson and Johnson, Ms. Foster held several senior human resources executive positions with Pfizer Inc., a publicly-tradedpublicly traded pharmaceuticals company, supporting its pharmaceuticals businesses in Japan, Asia, Africa, Middle East and Latin America and, notably, led the integration of both the Warner-Lambert and Pharmacia mergers for these regions. Prior to that, she gained 10 years of operational experience within The Yellow Pages. She currently serves on the board of directors and compensation committee of Prime Medicine, Inc., or Prime, a publicly traded biotechnology company, on the board of directors and compensation and community equity committee of National Resilience Inc., a technology-focused biomanufacturing company, on the board of directors and compensation and facilities committees of Stanford Health Care, a hospital and healthcare system, and also serves on the boardsboard and human resources committee of Spelman College and chairs the Board of Trustees of the Glide Memorial ChurchFoundation. Ms. Foster formerly served on the board of directors and Girls forcompensation committee of Grail, Inc., or Grail, a Change.private biotechnology company, prior to its acquisition by Illumina, Inc., or Illumina. She earned her undergraduate degree at Baruch College of the City University of New York and received her MBAM.B.A. from Columbia University, Graduate School of Business. We believe Ms. Foster’s qualifications to serve on our board of directors include her extensive experience as an executive in the pharmaceuticals industry.industry, including her experience in people management, compensation planning and driving and maintaining corporate culture.

Maykin Ho, Ph.D.has served as a member of our board of directors since June 2015. Dr. Ho has more than 30 years of experience in the healthcare and finance industries. She ishas been a retiredventure partner at Qiming Venture Partners, a venture capital firm in China and Hong Kong, since July 2015. From July 1992 to February 2015, she held various positions at Goldman Sachs, a global investment bank, including: from 2010 to 2015, she served as advisory director of the Goldman

Sachs Group whereglobal healthcare investment banking; from 2002 to 2010, she served as partner and co-head of healthcare investment research; and from 1992 to 2010 she served as senior biotechnology analyst, co-head of healthcare for global investment research and advisory director for healthcare investment banking. Previously,analyst. Prior to Goldman Sachs, Dr. Ho held various managerial positions in licensing, strategic planning, marketing and research at DuPont-Merck Pharmaceuticals, a global pharmaceutical company, and DuPont de Nemours & Company. She is a member of the board of directors and chairaudit committee of Fibrogen, Inc., a publicly traded biotechnology company; a member of the board of directors and audit committee forof Parexel International, a privately-held, global pharmaceutical services company; a member of the board of directors, audit committee and science and technology committee of BioMarin Pharmaceutical Inc., a publicly traded biopharmaceutical company; and a member of the board of directors, audit committee and nominating and governance committee of Neumora Therapeutics, Inc., a public biotechnology company. Dr. Ho previously served on the board of directors, audit committee and chaired the nominating and corporate governance committee of Grail, prior to its acquisition by Illumina in 2021. Dr. Ho also serves on the board of directors,

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audit committee and investment committee of two non-profit research institutes: the Aaron Diamond AIDS Research Center and the Institute for Protein Innovation. In addition, she is a non-profit organization in New York, and servesmember of the Biotech Advisory Panel of The Stock Exchange of Hong Kong. Previously, Dr. Ho served on the board of directors and audit committee of PAREXELParexel International when it was a publicly-traded multinational life sciences consulting firm. She also servedpublicly traded company, and on the investment committee of the Society of Neuroscience. Dr. HoShe was a postdoctoral fellow at the pathology department of Harvard Medical School and a graduate of the Advanced Management Program at The Fuqua School of Business, Duke University. SheDr. Ho received a Ph.D. in microbiology and immunology and a B.S. from the State University of New York, Downstate Medical Center. We believe Dr. Ho is qualified to serve on our board of directors due to her extensive experience in healthcare investment research and banking.

John M. Maraganore, Ph.D.Jeffrey Capello has served on our board of directors since June 2023. Mr. Capello has served as the managing partner of Monomoy Advisors, a financial advisory firm, since April 2021. Mr. Capello served as the Executive Vice President and Chief Financial Officer of Biogen Inc, a biopharmaceutical company, from December 2017 to August 2020. Prior to joining Biogen, Mr. Capello served as the Chief Financial Officer of Beacon Health Options, Inc., a behavioral health company, with responsibility for finance, human resources, information technology, real estate and procurement from October 2016 until November 2017. From July 2015 until September 2016, Mr. Capello was the founder and Chief Executive Officer of Monomoy Advisors. From July 2014 until June 2015 Mr. Capello served as the Executive Vice President and Chief Financial Officer of Ortho-Clinical Diagnostics, an in-vitro diagnostics company that was acquired by the Carlyle Group from Johnson & Johnson, with responsibility for global finance and business development. From March 2010 to December 2013 Mr. Capello served as Chief Financial Officer and Executive Vice President of Boston Scientific Corporation, a medical device company. Mr. Capello joined Boston Scientific in June 2008 and served as Senior Vice President and Chief Accounting Officer until March 2010. From 2006 to 2008 he was the Senior Vice President and Chief Financial Officer with responsibilities for global finance and business development at PerkinElmer, Inc., a life sciences tool company. Previously, he served as PerkinElmer’s Vice President of Finance, Corporate Controller, Treasurer and Chief Accounting Officer from 2001 to 2006. Prior to his tenure at PerkinElmer, Mr. Capello was a Partner at PricewaterhouseCoopers LLP, both in the United States and in the Netherlands. Mr. Capello serves on the board of directors of Neogen Corporation, a publicly traded company that develops solutions for food and animal safety, and previously served on the boards of directors and chaired the audit committees of public biotechnology companies Sirtis Pharmaceuticals, Inc., OvaScience, Inc. and Flex Pharma, Inc. Mr. Capello holds a M.B.A. from Harvard Business School and a B.S. in Business Administration from the University of Vermont. We believe that Mr. Capello is qualified to serve on our board of directors due to his over 30 years of industry experience, including extensive experience as a senior finance executive.

Catherine Owenhas served as a member of our board of directors since November 2011. SinceJune 2023. In her most recent role, Ms. Owen was Senior Vice President, Major Markets at Bristol-Myers Squibb, or BMS, a global biopharmaceutical company, overseeing commercial operations for the business in 18 countries including Japan, Germany, France, and others across Europe. Ms. Owen joined BMS in 2019 from Johnson & Johnson Corporation, or J&J, a healthcare company, where she served most recently as President of Janssen Immunology North America from 2018 to 2019, which launched new products in Crohn’s disease and psoriasis and led the development of J&J’s biosimilars strategy. Prior to leading Janssen Immunology, Ms. Owen was the President of the Infectious Diseases business in the US from 2016 to 2018, responsible for the HIV, RSV, Flu, and Hepatitis B pipeline. Prior to that Ms. Owen worked in various functions and businesses at J&J and led the launches of multiple products in both Europe and the United States. Ms. Owen began her career in the pharmaceutical industry in 1992 at AstraZeneca in London as a production support pharmacist. Ms. Owen was formerly on the board of directors and chair of the compensation committee for Optinose PLC, a public specialty pharmaceutical company, and was on the board of directors of Robert Wood Johnson University Hospitals, a non-profit organization. Ms. Owen earned her Bachelor of Science degree in pharmacy from the University of Manchester and completed her registered pharmacy degree and was a member of the Royal Pharmaceutical Society of Great Britain, MRPhs. We believe that Ms. Owen is qualified to serve on our board of directors because of her extensive commercial experience in the biotechnology industry.

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Members of the Board of Directors Continuing in Office

Term Expiring at the 2025

Annual Meeting of Stockholders (Class III)

Jacqualyn A. Fouse, Ph.D. served as our chief executive officer from February 2019 to August 2022, and has served as a member of our board of directors since December 2002,2017. Dr. MaraganoreFouse has served as the chiefchair of our board of directors since August 2022. Dr. Fouse served as executive officer and as a directorchair of Alnylam Pharmaceuticals,Dermavant Sciences, Inc., a publicly-traded biopharmaceutical company.company, from July 2017 until September 2018. From December 2002September 2010 until June 2017, Dr. Fouse served in various capacities at Celgene Corporation, a biopharmaceutical company, or Celgene, serving as strategic advisor to December 2007,the management executive committee from April 2017 to June 2017, president and chief operating officer from March 2016 to March 2017, president, hematology and oncology from August 2014 to February 2016, executive vice president and chief financial officer from February 2012 to July 2014, and senior vice president and chief financial officer from September 2010 to February 2012. Prior to joining Celgene, Dr. MaraganoreFouse served as presidentchief financial officer of Alnylam. From April 2000Bunge Limited, or Bunge, a global agribusiness and food company, from 2007 to December 2002,2010. Prior to joining Bunge, Dr. MaraganoreFouse served as senior vice president, strategic product developmentchief financial officer and corporate strategy at Alcon Laboratories, Inc., or Alcon, a global medical company, from 2006 to 2007, and as its senior vice president and chief financial officer from 2002 to 2006. Prior to her time with Millennium Pharmaceuticals. Before Millennium,Alcon she held a variety of senior leadership roles with international companies. Dr. Fouse is also a director and member of the audit and finance committee and nominating and corporate governance committee of Incyte Corporation, and was a director of Perrigo Company, a publicly traded pharmaceutical manufacturer, Celgene and Dick’s Sporting Goods, Inc., a publicly traded sporting goods retailer. Dr. Fouse also serves on the board of directors, and as Treasurer, of the non-profit organization Friends of Herring River and on the Northeast Chapter board of the non-profit organization the Society for Ecological Restoration. Dr. Fouse earned a B.A. and an M.A. in Economics and a Ph.D. in Finance from the University of Texas at Arlington. She also earned a Masters in Environmental Management from the Yale University School of Forestry and Environmental Studies. We believe Dr. Fouse is qualified to serve as a member of our board of directors due to her extensive experience in the biotechnology sector and her international and senior leadership experience.

David Scadden, M.D. has served as a member of our board of directors since May 2017. Dr. Scadden is a hematologist/oncologist and physician-scientist. He is the Gerald and Darlene Jordan Professor of Medicine at Harvard University, a position he has held since 2006. Since 1995, Dr. Scadden has practiced at the Massachusetts General Hospital, where he founded and directs the Center for Regenerative Medicine and directed the Hematologic Malignancies Center of the MGH Cancer Center for 10 years. Dr. Scadden co-founded and co-directs the Harvard Stem Cell Institute and is Chairman emeritus and Professor of the Harvard University Department of Stem Cell and Regenerative Biology. He is a member of the National Academy of Medicine, the American Academy of Arts and Sciences, is an affiliate member of the Broad Institute of Harvard and MIT and is a former member of the Board of External Experts for the National Heart, Lung and Blood Institute, the Board of Scientific Counselors for the National Cancer Institute, Board of Directors of the International Society for Stem Cell Research and the Executive Committee of the American Society of Hematology. Dr. Scadden is on the board of directors and organization, leadership and compensation and science and technology committees of Editas Medicine, Inc., a publicly traded biotechnology company, and on the boards of directors of the private biotechnology companies Lightning Biotherapeutics and Sonata Therapeutics. Dr. Scadden is also a scientific founder of Fate Therapeutics, Inc., a publicly traded biotechnology company, and was a scientific founder and member of the board of directors and scientific advisory board of Magenta Therapeutics, a publicly traded biotechnology company now merged with Dianthus Therapeutics, Inc. Dr. Scadden was also formerly on the boards of directors of the private biotechnology companies LifeVault Bio and Clear Creek Bio, Inc. He is the recipient of numerous honors including the E. Donnall Thomas and the Dameshek awards from the American

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Society of Hematology and awards from the Doris Duke Charitable Trust, the Ellison Medical Foundation, the Burroughs Welcome Fund, and the Leukemia and Lymphoma Society. Dr. Scadden holds degrees from Bucknell University, Case Western Reserve University and honorary degrees from Harvard University, Bucknell University and Lund University in Sweden. We believe Dr. Scadden is qualified to serve on our board of directors due to his scientific expertise in the field of hematology.

David P. Schenkein, M.D. has served as a member of our board of directors since August 2009, as our executive chairman from February 2019 to February 2020, and as the chair of our board of directors from February 2020 to August 2022. Dr. Schenkein also served as our president and chief executive officer from August 2009 until February 2019. Dr. Schenkein has been a hematologist and medical oncologist for more than 30 years. He currently serves as a general partner of GV (Google Ventures), the venture capital arm of Alphabet Inc. (formerly Google), and is an adjunct attending physician in hematology at Tufts Medical Center. Prior to joining Agios, from 2006 to 2009, Dr. Schenkein was the senior vice president, clinical hematology/oncology at Genentech Inc. (now a member of the Roche Group, a global healthcare company), or Genentech, where he was responsible for numerous successful oncology drug approvals and leading the medical and scientific strategies for its bio-oncology portfolio. While at Genentech, he served as directoran adjunct clinical professor of molecular biology and directormedical oncology at Stanford University School of market and business development at Biogen.Medicine. Prior to Biogen,joining Genentech, he served as the senior vice president of clinical research at Millennium, overseeing the clinical development and worldwide approval of VELCADE^®, a first-in-class cancer therapy now approved to treat multiple myeloma and non-Hodgkins lymphoma. Dr. MaraganoreSchenkein currently serves on the board of directors of Leyden Labs, Inc., Aera Therapeutics, Inc., or Aera, and Treeline Biosciences, all private biotechnology companies, and on the board of directors, nominating and corporate governance committee and science and technology committee of Denali Therapeutics Inc., a publicly traded biotechnology company, on the board of directors, compensation committee and nominating and corporate governance committee of Prime, and on the board of directors and technology committee of Regeneron Pharmaceuticals, Inc., a publicly traded biotechnology company. Dr. Schenkein was formerly on the board of directors of Foundation Medicine, Inc., a scientistpublicly traded biotechnology company and on the board of directors, compensation committee and nominating and corporate governance committee of bluebird bio, or bluebird, a publicly traded biotechnology company. Dr. Schenkein holds a B.A. in chemistry from Wesleyan University and an M.D. from the State University of New York Upstate Medical School. We believe that Dr. Schenkein’s detailed knowledge of our company and of hematology and his extensive background in the biotechnology industry, including his roles at ZymoGenetics,Genentech and Millennium, provide a critical contribution to our board of directors.

Term Expiring at the 2026

Annual Meeting of Stockholders (Class I)

Rahul Ballal, Ph.D. has served as a member of our board of directors since August 2022. Dr. Ballal has served as chief executive officer of Mediar Therapeutics Inc., or Mediar, a private biotechnology company, since March 2023. Prior to that, he served as President and Chief Executive Officer of Imara, Inc. or Imara, a publicly traded biotechnology company, from June 2018 until its merger with Enliven Therapeutics, Inc., or Enliven, a public biotechnology company in February 2023. Prior to joining Imara, Dr. Ballal served as Chief Business Officer of Northern Biologics Inc., a biotechnology company, from May 2016 to June 2018, and The Upjohn Company,as an Entrepreneur-in-Residence at Versant Ventures Management LLC, a pharmaceutical manufacturing company.life sciences venture capital firm. Previously, Dr. Maraganore is a director of bluebird bio,Ballal was Vice President, Business Development at Flexion Therapeutics, Inc., or Flexion, a publicly-tradedpublicly traded biopharmaceutical company, and Tempero Pharmaceuticals, a majority-owned subsidiary and affiliate of GlaxoSmithKline. In addition,from March 2011 to May 2016. Prior to Flexion, he was formerlyheld a venture partnerfellowship position at Third Rock Ventures, L.P., where he participatedNovartis Venture Funds, a venture capital fund, as part of the Kauffman Fellowship, from June 2010 to June 2012, and overlapped in business development at the Broad Institute of Massachusetts Institute

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of Technology, a limited capacity focusingbiomedical and genomic research center. Dr. Ballal was also the founder and CEO of Redmind LLC, a venture backed data analytics startup that was sold to Ikimbo Inc. in June 2002. Dr. Ballal serves on guiding strategy for Third Rock and its portfolio companies, and was formerly chairman of the board of directors of RegulusMediar, on the board of directors of Enliven, and on the board of directors of Vaderis Therapeutics Inc.,AG, a publicly-tradedprivate biotechnology company. HeDr. Ballal also serves on the board of directors and audit and risk committee of The Park School, a non-profit organization. Dr. Ballal received his Ph.D. in biochemistry and molecular biology from Georgetown University, his M.S. in biotechnology from Johns Hopkins University and his B.A. in biology from Brown University. We believe Dr. Ballal is alsoqualified to serve on our board of directors based on his broad experience in the life sciences industry, including in various investment, operating and leadership roles.

Brian Goff has served as our chief executive officer and a member of our board of directors since August 2022. Prior to joining Agios, Mr. Goff served as Executive Vice President, Chief Commercial and Global Operations Officer of Alexion Pharmaceuticals, Inc. or Alexion, from June 2017 to July 2021. Mr. Goff led the Immunology Advisory Councilglobal commercial and operations teams at Alexion, which included responsibility for country operations in each of Harvard Medical SchoolAlexion’s affiliates in North America, EMEA, Japan, Asia Pacific, and Latin America. Prior to joining Alexion in June 2017, Mr. Goff was Chief Operating Officer and a member of the board of directors of Neurovance, Inc., a biopharmaceutical company, from December 2016 until its acquisition by Otsuka Pharmaceuticals Co., Ltd. in March 2017. Prior to joining Neurovance, Mr. Goff served as the Biotechnology Industry Organization. Dr. Maraganore holdsExecutive Vice President & President — Hematology Division of Baxalta Incorporated, a biopharmaceutical company, from January 2015 to July 2016 until its acquisition by Shire plc. He previously served with Baxter Healthcare Corporation as Global Hemophilia Franchise Head from June 2012 to December 2014. Earlier in his career, Mr. Goff held positions of increasing responsibility in sales and marketing roles with Novartis Pharmaceuticals, and the pharmaceutical division of Johnson & Johnson. Mr. Goff has an M.S.M.B.A. from the Wharton School at the University of Pennsylvania and a Ph.D.B.A. from Skidmore College. We believe Mr. Goff is qualified to serve as a member of our board of directors due to his more than 30 years of industry experience, including executive commercial leadership experience in Biochemistryrare diseases and Molecular Biologyinternational operations.

Cynthia Smith has served as a member of our board of directors since August 2022. Since January 2017, Ms. Smith has consulted as a strategic advisor for biotechnology companies. Previously, she served as Chief Commercial Officer and a member of the Executive Committee of ZS Pharma, Inc., or ZS Pharma, a specialty pharmaceutical company developing therapies for treatment of hyperkalemia and liver diseases, from 2013 to 2016, where she led efforts to transition the company from a development stage company to a commercial enterprise. ZS Pharma was acquired by AstraZeneca in 2015. Prior to ZS Pharma, Ms. Smith served as Vice President, Market Access and Commercial Development at Affymax, Inc., a biopharmaceutical company, from 2008 to 2013. From 2000 to 2008, she held various senior leadership positions in market access, corporate strategy, government relations and external affairs at Merck & Co. Before beginning her career in the biopharmaceutical industry, Ms. Smith served as a healthcare policy analyst in the Office of Management and Budget at the White House from 1995 to 2000. Ms. Smith currently serves on the boards of directors of publicly traded biotechnology companies Akebia Therapeutics, Inc. Protara Therapeutics, Inc., and Spero Therapeutics, Inc., and on the board of directors of the French-American Foundation. Ms. Smith previously served on the board of directors of Nivalis Therapeutics, Inc. from November 2016 to July 2017 and on the board of directors of Dicerna Pharmaceuticals, Inc. from August 2018 until its acquisition by Novo Nordisk A/S in 2021. Ms. Smith earned a B.A. from the University of Chicago and a B.A. in Biological Sciences alsoNorth Carolina at Chapel Hill, an M.B.A. from the UniversityWharton School and an M.S. in public policy from the Eagleton Institute of Chicago. Dr. Maraganore has over 25 years of experience in the biotechnology industry, bringingPolitics at Rutgers University. We believe that Ms. Smith is qualified to serve on our board critical scientific, research and development, and general management expertise.

Recommendation of the Board of Directors

OUR BOARD OF DIRECTORS UNANIMOUSLY RECOMMENDS THAT THE STOCKHOLDERS VOTE FOR THE ELECTION OF EACH OF MS. FOSTER, DR. HO, MR. CAPELLO AND MS. OWEN.

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CORPORATE GOVERNANCE

General

We believe that good corporate governance is important to ensure that Agios Pharmaceuticals, Inc. is managed for the long-term benefit of our stockholders. This section describes key corporate governance practices that we have adopted. We have adopted a code of business conduct and ethics, which applies to all of our officers, directors and employees, corporate governance guidelines and charters for our audit committee, our compensation & people committee, our nominating and corporate governance committee and our science and technology committee. We have posted copies of our code of business conduct and ethics and corporate governance guidelines, as well as each of our committee charters, on the Corporate Governance page of the Investors & Media section of our website, www.agios.com, which you can access free of charge. Information contained on the website is not incorporated by reference in, or considered part of, this proxy statement.Proxy Statement. We intend to disclose on our website any amendments to, or waivers from, our code of business conduct and ethics that are required to be disclosed by law or NASDAQNasdaq listing standards. We will also provide copies of these documents, as well as our other corporate governance documents, free of charge, to any stockholder upon written request to Renee Leck, Investor Relations, at 88 Sidney Street, Cambridge, MA 02139,Massachusetts 02139; telephone: 617-649-8600;e-mail: renee.leck@agios.com. IR@agios.com.

Corporate Governance Guidelines

Our Boardboard of directors has adopted corporate governance guidelines to assist in the exercise of its duties and responsibilities and to serve the best interests of Agios and our stockholders. These guidelines, which provide a framework for the conduct of our board’s business, provide that:

Corporate Social Responsibility

We are committed to building a sustainable business that provides long-term value for all our stakeholders. Central to our mission is our drive to improve the lives of those fighting life-threatening and life-altering rare diseases, including those that have often been overlooked or neglected. We also support and advance a range of other responsibilities, such as: increasing access to medicines; advancing diversity, equity, and inclusion both internally and externally; building a strong culture of flexibility and respect; creating opportunities in STEM; promoting health equity; reducing our waste and energy usage; making a difference in our communities; and conducting our business according to the highest ethical standards.

Since 2020, we have published our Environmental, Social, and Governance (ESG) Report, with the intent of disclosing relevant ESG initiatives and metrics from across the company that are aligned not only with our

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Director Determination of Independence

Rule 5605 of the NASDAQNasdaq Listing Rules requires a majority of a listed company’s board of directors to be comprised of independent directors within one year of listing.directors. In addition, the NASDAQNasdaq Listing Rules require that, subject to specified exceptions, each member of a listed company’s audit, compensation and nominating and corporate governance committees be independent, that audit committee members also satisfy independence criteria set forth in Rule 10A-3 under the Securities Exchange Act of 1934, as amended, or the Exchange Act and that compensation committee members also satisfy the independence criteria set forth in Rule 10C-1 under the Exchange Act.

Under Rule 5605(a)(2) of the NASDAQNasdaq Listing Rules, a director will only qualify as an “independent director” if, in the opinion of oura company’s board of directors, that person does not have a relationship that would interfere

with the exercise of independent judgment in carrying out the responsibilities of a director. In order to be considered independent for purposes of Rule 10A-3 of the Exchange Act, a member of an audit committee of a listed company may not, other than in their capacity as a member of the audit committee, the board of directors, or any other board committee, accept, directly or indirectly, any consulting, advisory, or other compensatory fee from the listed company or any of its subsidiaries or otherwise be an affiliated person of the listed company or any of its subsidiaries.

In addition, in affirmatively determining the independence of any director who will serve on a company’s compensation committee, Rule 10C-1 under the Exchange Act requires that a company’s board of directors consider all factors specifically relevant to determining whether a director has a relationship to such company which is material to that director’s ability to be independent from management in connection with the duties of a compensation committee member, including, but not limited to: (i) the source of compensation of the director, including any consulting advisory or other compensatory fee paid by such company to the director; and (ii) whether the director is affiliated with the company or any of its subsidiaries or affiliates.

OurIn March 2024, our board of directors undertook a review ofreviewed the composition of our board of directors and its committees and the independence of each director. Based upon information requested from and provided by each director concerning his or her background, employment and affiliations, including family relationships, our board of directors has determined that each of our directors with the exception of Drs. Schenkein and Cantley and Mr. Karsen, who resigned from our board of directors effective March 1, 2016, is an “independent director” as defined under Rule 5605(a)(2) of the NASDAQNasdaq Listing Rules.Rules, with the exception of Mr. Goff, our chief executive officer, and Dr. Fouse, our chair. Our board of directors had also previously determined that John Maraganore, a former director who resigned from our board of directors in May 2023, and Paul Clancy, a former director who did not

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stand for re-election at the 2023 annual meeting of stockholders, were each “independent directors” as defined under Rule 5605(a)(2). In addition, our board of directors determined that Dr. Ballal, Mr. ClancyCapello and Drs. Cole and Maraganore,Dr. Ho, who currently comprise our audit committee, Ms. Foster, Dr. MaraganoreMs. Owen and Mr. Nelsen,Ms. Smith, who currently comprise our compensation & people committee, and Dr. Cole, Ms. Foster, Dr. Ho and Dr. Ho,Scadden, who are members ofcurrently comprise our nominating and corporate governance committee, satisfy the independence standards for such committees established by the Securities and Exchange CommissionSEC and the NASDAQNasdaq Listing Rules, as applicable. In making such determinations, our board of directors considered the relationships that each such non-employee director has with our company, including any relevant transactions described below in “Certain Relationships and Related Party Transactions” and the beneficial ownership of our capital stock by each non-employee director, as well as all other facts and circumstances our board of directors deemed relevant in determining independence. Mr. Goff is not independent because he is our chief executive officer. Dr. Fouse is not independent because she previously served as our chief executive officer within the past three years.

Board Leadership Structure

Our corporate governance guidelines provide that the nominating and corporate governance committee shall periodically assess our board of directors’ leadership structure, including whether the offices of chief executive officer and chair of the board of directors should be separate and why the board of directors’ leadership structure is appropriate given the specific characteristics or circumstances of our company. These guidelines provide the board of directors with flexibility to determine whether the two roles should be combined or separated based upon our needs and the board of directors’ assessment of its leadership from time to time. We currently separate the roles of chief executive officer and chair of the board of directors. Separating the duties of the chair of the board from the duties of the chief executive officer allows our chief executive officer to focus on our day-to-day business, while allowing the chair of the board to lead the board of directors in its fundamental role of providing advice to and independent oversight of management. Specifically, the chair of our board of directors presides over meetings of the board of directors, facilitates communications between management and the board of directors, provides input on the design of the board of directors and assists with other corporate governance matters.

Because Dr. Fouse, the chair of our board of directors is not independent within the meaning of the Nasdaq Listing Rules, our board of directors, upon the recommendation of our nominating and corporate governance committee, has determined that the roles of chairman of the board and chief executive officer should be separated at the current time. Accordingly, our Board has appointed Dr. Tessier-Lavigne,Ms. Foster as lead independent director. Ms. Foster is an independent director within the meaning of NASDAQthe Nasdaq Listing Rules (see “Director Determination of Independence” above), as the chairman of the board of directors. Dr. Tessier-Lavigne possesses an in-depth knowledge of our issues, opportunities and challenges. We believe he is the person best positioned to ensure our board of directors’ time and attention is focused on the most critical matters. Our board of directors believes Dr. Tessier-Lavigne is a decisive leader who commands accountability and enhances our ability to communicate our message and strategy clearly and consistently to stockholders, employees and strategic partners. Dr. Tessier-Lavigne’s. Her duties as chairman of the boardlead independent director include the following: