Table of Contents

PROPOSAL 2: AMENDMENT TO THE COMPANY’S RESTATED CERTIFICATE OF INCORPORATION TO INCREASE THE NUMBER OF AUTHORIZED SHARES OF COMMON STOCK FROM 125,000,000 TO 250,000,000

​

On March 23, 2021, upon the recommendation of our Nominating and Corporate Governance Committee, our Board approved the adoption of and declared advisable to the Company and its stockholders, subject to stockholder approval, an amendment to the Company’s Restated Certificate of Incorporation, or the Restated Certificate, to increase the number of authorized shares of common stock, par value $0.001 per share, from 125,000,000 shares to 250,000,000 shares. The proposed amendment to the Restated Certificate would not increase or otherwise affect our authorized preferred stock.

Our Board believes it is in the best interest of the Company and its stockholders to increase the number of authorized shares of common stock to give the Company greater flexibility in considering and planning for future potential business needs and pursuing our strategic goals. We currently have no specific plans, arrangements or understandings to issue additional shares of our common stock, except for the issuance of shares of common stock pursuant to our equity incentive plans to persons eligible to participate in those plans, including pursuant to the proposed amendment to our 2016 Employee Stock Purchase Plan, and potential future issuances pursuant to our at-the-market sales agreement with Cantor Fitzgerald & Co. and RBC Capital Markets, LLC, dated August 7, 2019, or our at-the-market sales agreement. However, the availability of additional shares of common stock for issuance is, in the Board's view, prudent and will afford the company with flexibility in acting upon financing transactions to strengthen our financial position and/or commercial partnership opportunities that may arise. The increase in the number of authorized but unissued shares of common stock would enable our Board, without the expense and delay of seeking stockholder approval, to issue shares from time to time as may be required for proper business purposes. The additional shares of common stock will be available for issuance by our Board for various corporate purposes, including but not limited to, grants under our equity incentive award plans, financings such as public or private offerings of common stock or convertible securities, including issuances under our at-the-market sales agreement, satisfaction of potential milestone payment obligations, potential settlement of conversions of our 3.00% convertible senior notes due August 15, 2022 and our 1.50% convertible senior notes due September 15, 2026, potential strategic transactions, including mergers, acquisitions, strategic partnerships, collaborations, strategic investments, joint ventures, divestitures, business combinations, stock splits, stock dividends as well as other general corporate transactions and other corporate purposes that have not yet been identified. If the authorization of an increase in the available common stock is postponed until the foregoing specific needs arise, the delay and expense incident to obtaining approval of the stockholders at that time could impair our ability to achieve the corporate purposes set forth above.

The Restated Certificate currently authorizes the issuance of up to 125,000,000 shares of common stock, par value $0.001 per share, and 5,000,000 shares of preferred stock, par value $0.001 per share. As of April 16, 2021, 70,418,067 shares of our common stock were outstanding and our Board had reserved 12,623,895 shares of common stock for issuance upon the exercise of outstanding stock options and unvested restricted stock units, 752,366 shares of common stock for issuance pursuant to our 2013 Long Term Incentive Plan, 1,096,710 shares of common stock for issuance pursuant to our 2020 Inducement Stock Incentive Plan, as amended, and 359,167 shares of common stock for issuance pursuant to our 2016 Employee Stock Purchase Plan. In addition, our Board has reserved up to 10,577,310 shares of common stock for issuance upon conversion of our 3.00% convertible senior notes due August 15, 2022 and our 1.50% convertible senior notes due September 15, 2026. As a result, the Company has only 29,172,485 shares of common stock available for future issuance out of the 125,000,000 shares of common stock currently authorized as of March 31, 2021. Additionally, we have the option to pay our contingent obligations of (i) up to $200.0 million in potential milestone payments to BioElectron pursuant to an Asset Purchase Agreement by and between us and BioElectron, dated October 1, 2019 and (ii) a $30.0 million development milestone payment upon the completion of enrollment of a Phase 3 clinical trial for PTC923 for PKU to former Censa securityholders pursuant to an Agreement and Plan of Merger, dated as of May 5, 2020, by and among us, Hydro Merger Sub, Inc., our wholly owned, indirect subsidiary, and, solely in its capacity as the representative, agent and attorney-in-fact of the securityholders of Censa, Shareholder Representatives Services LLC, in shares of our common stock rather than in cash. Our Board has also approved, and we are seeking stockholder approval of, an increase of 1,000,000 shares of common stock to be reserved for issuance under the 2016 Employee Stock Purchase Plan, as described in Proposal 3.

Table of Contents

If this proposal is approved, the additional authorized shares may be issued at the discretion of our Board without further stockholder action, except as may be required by law or the rules of Nasdaq. The adoption of the proposed amendment to the Restated Certificate would not have any immediate dilutive effect on the proportionate voting power or other rights of existing stockholders. However, the issuance of shares of common stock, other than on a pro-rata basis to all stockholders, would reduce each stockholder’s proportionate interest in the Company and the issuance of additional shares of common stock may, among other things, have a dilutive effect on earnings per share and on stockholders' equity and voting rights. Furthermore, future sales of substantial amounts of our common stock, or the perception that these sales might occur, could adversely affect the prevailing market price of our common stock or limit our ability to raise additional capital. Stockholders should recognize that, as a result of this proposal, they will own a smaller percentage of shares relative to the total authorized shares of the company than they presently own. The holders of any of the additional shares of common stock issued in the future would have the same rights and privileges as the holders of the shares of common stock currently authorized and outstanding. Those rights do not include preemptive rights with respect to the future issuance of any additional shares. The holders of shares of our common stock will have no dissenters' rights of appraisal under Delaware law, our Restated Certificate or our Bylaws with respect to the proposed amendment to the Restated Certificate.

The issuance of additional shares of common stock could have the effect of making it more difficult for a third party to acquire, or discouraging a third party from attempting to acquire, control of the company. We are not aware of any attempts on the part of a third party to effect a takeover of the company, and the proposed amendment to the Restated Certificate has been proposed for the reasons stated above and not with the intention that any increase in the authorized shares of common stock be used as a type of anti-takeover device.

A copy of the proposed amendment to the Restated Certificate is attached as Exhibit A to this proxy statement. If the proposed amendment to the Restated Certificate is approved, subject to the discretion of the Board of Directors, as soon as practicable after the Annual Meeting, the Company will file the amendment to the Restated Certificate with the office of the Secretary of State of Delaware to reflect the increase in the authorized number of shares of our common stock. Upon approval and following such filing with the Secretary of State of Delaware, the amendment to the Restated Certificate will become effective on the date it is filed. Our Board reserves the right to abandon or delay the filing of the amendment to the Restated Certificate even if it is approved by the stockholders. If the proposed amendment to the Restated Certificate is approved and becomes effective, the first paragraph of Article FOURTH of our Restated Certificate, which sets forth our currently authorized capital stock, will be amended to read in its entirety as follows:

“FOURTH: The total number of shares of all classes of stock which the Corporation shall have authority to issue is Two Hundred Fifty-Five Million (255,000,000) shares, consisting of (i) Two Hundred Fifty Million (250,000,000) shares of Common Stock, $0.001 par value per share (“Common Stock”), and (ii) Five Million (5,000,000) shares of Preferred Stock, $0.001 par value per share (“Preferred Stock”).”

The affirmative vote of the holders of at least a majority of the shares of common stock entitled to vote at the Annual Meeting will be required to approve this proposal. Abstentions will have the practical effect of a vote against the amendment to the Restated Certificate. Our Board urges stockholders to vote for this proposal as failure to obtain the vote of a majority of outstanding shares may limit the Company’s abilities to operate and execute on future business plans.

Our Board Recommends that You Vote "FOR" the Approval of an Amendment to the Company’s Restated Certificate of Incorporation to Increase the Number of Authorized Shares of Common Stock from 125,000,000 to 250,000,000.

​

Table of Contents

PROPOSAL 3: AMENDMENT TO THE COMPANY’S 2016 EMPLOYEE STOCK PURCHASE PLAN TO INCREASE THE NUMBER OF AUTHORIZED SHARES OF COMMON STOCK UNDER THE PLAN FROM 1,000,000 TO 2,000,000

On March 23, 2021, upon the recommendation of our Compensation Committee, our Board approved the adoption of and declared advisable to the Company and its stockholders, subject to stockholder approval, an amendment to the Company’s 2016 Employee Stock Purchase Plan, or the ESPP, to increase the number of authorized shares of common stock authorized for issuance under the ESPP from 1,000,000 shares to 2,000,000 shares (we refer to the ESPP as so amended, as the Amended ESPP).

A description of the material terms of the Amended ESPP are summarized below. The only difference between the terms of the ESPP and the Amended ESPP is that the Amended ESPP provides that an additional 1,000,000 shares of our common stock may be issued pursuant to the Amended ESPP.

The Amended ESPP is intended to benefit our company and our stockholders by attracting, retaining and motivating talented employees, which we believe to be critical for our success, and aligning the interests of participating employees with our stockholders. We believe that the ability to participate in the Amended ESPP is an attractive feature for current and potential employees by affording them the opportunity to share in the growth and success of the Company. The Amended ESPP also helps to attract and retain employees because employee stock purchase plans are commonly offered by our peers and other industry leaders. In 2018, 2019 and 2020, we issued a total of 139,181, 107,145 and 124,736 shares of common stock under the ESPP, respectively. As of April 16, 2021, 359,167 shares were available for future issuance under the ESPP without giving effect to the approval of the Amended ESPP. As our employee population continues to grow, if the Amended ESPP is not approved by our stockholders, our ability to recruit and retain employees could be negatively impacted if we do not have sufficient authorized shares available for future issuance under our ESPP for our employees’ participation. To further encourage stock ownership among our employees while providing our employees a benefit that is common in the companies with which we compete for talent, our Board has adopted the Amended ESPP.

A majority of the voting power of the shares of common stock cast on this matter is required to approve this proposal. Our Board urges stockholders to vote for this proposal as failure to obtain the required vote may limit the Company’s ability to attract, retain and motivate talented employees.

Our Board Recommends that You Vote "FOR" the Approval of an Amendment to the Company’s 2016 Employee Stock Purchase Plan to Increase the Number of Authorized Shares of Common Stock under the Plan from 1,000,000 to 2,000,000.

Description of the Amended ESPP

The following is a brief summary of the Amended ESPP. The following description is only a summary of the material terms of the Amended ESPP, and is qualified in its entirety by reference to the Amended ESPP, a copy of which is attached to this proxy statement as Exhibit B. You can request a copy of the Amended ESPP by writing to PTC Therapeutics, Inc., Attn: Corporate Communications, 100 Corporate Court, South Plainfield, New Jersey 07080. A copy of the Amended ESPP, which is attached to the electronic copy of this proxy statement filed with the SEC, also may be accessed from the SEC's home page (www.sec.gov).

Eligibility

All employees of the Company and any subsidiary of the Company designated by our Board or Compensation Committee are eligible to participate in the Amended ESPP provided that they work more than twenty (20) hours per week and for more than five (5) months in a calendar year, are employees for at least two (2) years prior to enrolling in the Amended ESPP and are employees on the first day of the applicable offering period; provided, that we may permit employees who work fewer hours per week, fewer months per calendar year or who have been employed for a shorter period of time prior to participating in the Amended ESPP, in accordance with the terms of the Amended ESPP, Section 423 of the Code and guidelines that we establish under the Amended ESPP. No employee can be granted an option under

Table of Contents

the Amended ESPP that would result in the employee owning common stock and/or options to purchase common stock representing five percent or more of the total combined voting power or value for all classes of our outstanding capital stock. As of March 31, 2021, approximately 957 employees would have been eligible to participate in the Amended ESPP, including our currently employed named executive officers.

Amended ESPP Operation

The Amended ESPP permits eligible employees to purchase shares of our common stock at a discount. Eligible employees may elect to participate by completing an enrollment form, timely filing it with our payroll office and authorizing after-tax payroll deductions from their pay. Participants can elect to contribute from 1 to 15 percent (or such higher or lower maximum percentage as we may determine in accordance with the terms of the Amended ESPP, Section 423 of the Code and guidelines that we establish under the Amended ESPP), in whole percentages only, of their compensation (as defined in the Amended ESPP) received on each pay day during the offering period. Our Board or Compensation Committee may also, in its discretion, establish a different minimum payroll deduction percentage.

The Amended ESPP will be implemented by consecutive six (6) month offering periods. Our Board or Compensation Committee may, in its discretion, choose a different offering period of not more than twenty-seven (27) months.

Offering periods will begin at such time as our Compensation Committee may determine and establish in the Amended ESPP's guidelines. The guidelines currently contemplate that offering periods will begin on the first day on which national stock exchanges and Nasdaq are open for trading on or after July 1 and January 1 of each year. On the first day of each offering period, each employee who is enrolled in the Amended ESPP will automatically receive an option to purchase, on the last business day of the offering period, up to that number of shares of our common stock determined by multiplying $2,083 by the number of full months in the plan period and dividing the result by the closing price of our common stock on the first day of the offering period, or such lesser number of shares set by the Board or Compensation Committee. We refer to these as the option shares.

However, no eligible employee may be granted an option under the Amended ESPP that permits the employee's rights to purchase shares under the Amended ESPP to accrue at a rate that exceeds $25,000 in fair market value (based on the value of the stock on the first day of the offering period) of our common stock in any given calendar year in which such option is outstanding at any time.

Unless a participant withdraws from the Amended ESPP, the participant's option will be exercised automatically on the last business day of the offering period as to the largest whole number of shares that are exercisable and can be purchased with the deductions accumulated as of the last business day of the offering period.

Our Board or Compensation Committee will determine the purchase price of each of the shares purchased in a given offering period. The purchase price will be at least 85% of (i) the closing price of a share of our common stock on the first business day of the offering period or the last business day of the offering period, whichever is lower or (ii) the closing price of a share of our common stock on the last business day of the offering period. If the total number of shares of common stock with respect to which options are to be exercised exceeds the number of shares remaining available for issuance under the Amended ESPP, we will only issue to participants in that offering that number of shares remaining available for issuance, on a pro-rata basis.

All payroll deductions received or held by the Company under the Amended ESPP may be used by us for any corporate purpose, and we will not be obligated to segregate such payroll deductions. No interest will accrue on the payroll deductions (except as our Board or Compensation Committee may otherwise provide), and an employee participating in the Amended ESPP may not increase or decrease payroll deductions, except as permitted by the Amended ESPP. Employees may purchase common stock under the Amended ESPP only through payroll deductions. A participant's payroll deduction elections remain in effect for successive offering periods. Except to the extent provided by our Board or Compensation Committee in accordance with the Amended ESPP, Section 423 of the Code and guidelines with respect to the Amended ESPP a participant's payroll deduction may be decreased, increased or terminated by the participant only with respect to the next offering period. A participant may decrease or increase the

Table of Contents

rate of his or her payroll deductions for subsequent offering periods by filing a new enrollment form with our payroll office authorizing a change in payroll deduction rate. In addition, a participant may elect to discontinue his or her payroll deductions during an offering period but not elect to withdraw his or her funds. In such cases, funds deducted prior to his or her election to discontinue shall be applied to the purchase of common stock on the last day of the purchase period in which the funds were deducted. If an employee withdraws from participation during an offering period, the amounts contributed to the Amended ESPP will be refunded promptly without interest and the employee's option granted for such offering period will automatically terminate. At the end of the offering period, the accumulated payroll contributions of each employee who continues to participate in the plan as of such date will be used to purchase shares of common stock (at the option price described above) subject to the limitations described above. A participant's withdrawal from an offering period will not have any effect upon his or her eligibility to participate in succeeding offering periods or in any other similar plan which the Company may adopt.

The value of the common stock purchased will vary based on the fair market value of our common stock on the last day of the offering period. Accordingly, the dollar value and the number of shares that may be purchased in the future pursuant to the Amended ESPP are not currently determinable.

We are required to make equitable adjustments to the number and class of securities available under the Amended ESPP, the share limitations under the Amended ESPP and the purchase price for an offering period under the Amended ESPP to reflect stock splits, reverse stock splits, stock dividends, recapitalizations, combinations of shares, reclassifications of shares, spin-offs and other similar changes in capitalization or events or any dividends or distributions to holders of our common stock other than ordinary cash dividends.

In connection with a merger or other reorganization event (as defined in the Amended ESPP), our Board or a committee appointed by our Board may take any one or more of the following actions as to outstanding options to purchase shares of our common stock under the Amended ESPP on such terms as our Board or committee determines:

​

Table of Contents

Administration

The Amended ESPP shall be administered by our Board or by a committee appointed by the Board. Our Board or such committee has authority to make rules and regulations for the administration of the Amended ESPP, and its interpretation and decisions with respect to the Amended ESPP shall be final and conclusive.

The Board or such committee may delegate to one or more officers of the Company the authority to implement and administer the Amended ESPP, subject to the terms of the Amended ESPP and any guidelines approved by the Board or such committee. The Board has appointed the Compensation Committee to administer the ESPP, and the Compensation Committee has delegated authority over certain administrative matters with respect to the ESPP to the Company's Employee Benefit Plan Committee, subject to the terms of the ESPP and the guidelines adopted by the Compensation Committee. Such delegations will remain in effect if the Amended ESPP is approved by the stockholders.

Our Board or Compensation Committee has the ability to change offering periods (including the commencement dates and length thereof) with respect to future offerings without stockholder approval. Our Board may terminate or amend the Amended ESPP at any time and for any reason. The Board may amend the Amended ESPP at any time, but the plan may not be amended in any way that will cause rights issued thereunder to fail to meet the requirements for employee stock purchase plans as defined in Section 423 of the Code including stockholder approval if required.

Our Board or the Compensation Committee may allow employees who are citizens or residents of foreign jurisdictions to participate in an offering period or establish sub-plans for the benefit of such foreign employees to the extent such actions are in compliance with Section 423 of the Code.

New Plan Benefits

Benefits and purchases of shares of our common stock under the Amended ESPP depend on elections made by employees and the fair market value of our common stock on dates in the future. As a result, it is not possible to determine the benefits that will be received by executive officers and other employees in the future under the Amended ESPP.

For illustrative purposes only, the following table sets forth certain information regarding the number of shares of our common stock purchased during the fiscal year 2020 offering periods pursuant to our ESPP by each of (i) the NEOs identified in the Summary Compensation Table of this proxy statement, (ii) all current executive officers, as a group, and (iii) all employees, other than executive officers, as a group. Non-executive members of our Board are not eligible to participate in the ESPP.

Table of Contents

Since the ESPP was approved by our stockholders in 2016: Dr. Peltz has purchased 0 shares of our common stock under the ESPP, Ms. Hill has purchased 0 shares of our common stock under the ESPP, Dr. Almstead has purchased 2,490 shares of our common stock under the ESPP, Mr. Boulding has purchased 2,490 shares of our common stock under the ESPP, Mr. Pauwels has purchased 3,774 shares of our common stock under the ESPP, Mr. Souza has purchased 3,505 shares of our common stock under the ESPP, all of our current executive officers, as a group have purchased 13,068 shares of our common stock under the ESPP, all of our non-executive directors and director nominees, as a group have purchased 0 shares of our common stock under the ESPP and all of our employees, other than current executive officers, as a group have purchased 627,765 shares of our common stock under the ESPP.

​

Federal Income Tax Consequences

The following generally summarizes the United States federal income tax consequences that will arise with respect to participation in the Amended ESPP and with respect to the sale of common stock acquired under the plan. This summary is based on the tax laws in effect as of the date of this proxy statement. The Amended ESPP is intended to qualify as an "employee stock purchase plan" as defined in Section 423 of the Code. This summary assumes that the Amended ESPP complies with Section 423 of the Code. Further, this summary assumes that the purchase price for shares is 85% of the closing price of a share of our common stock on the first day of the offering period or the last day of the offering period, whichever is lower. Changes to these laws could alter the tax consequences described below.

Tax Consequences to Participants

A participant will not have income upon enrolling in the Amended ESPP or upon purchasing stock at the end of a purchase period. A participant may have both compensation income and a capital gain or loss upon the sale of stock that was acquired under the Amended ESPP. The amount of each type of income and loss will depend on whether the participant disposes of the stock in a qualifying or disqualifying disposition. A qualifying disposition is when the participant sells the stock more than two years after the commencement of the offering during which the stock was purchased and more than one year after the date on which the participant purchased the stock at a profit (i.e., the sales proceeds exceed the purchase price). In a qualifying disposition, the participant will have compensation income equal to the lesser of:

Any profit in excess of compensation income will be long-term capital gain. If the participant sells the stock at a loss (i.e., if sales proceeds are less than the purchase price) after satisfying these waiting periods, then the loss will be a long-term capital loss.

If the participant sells the stock prior to satisfying these waiting periods, then he or she will have engaged in a disqualifying disposition. Upon a disqualifying disposition, the participant will have compensation income equal to the value of the stock on the day he or she purchased the stock less the purchase price. The participant also will have a capital gain or loss equal to the difference between the sales proceeds and the value of the stock on the day he or she purchased the stock. This capital gain or loss will be long-term if the participant has held the stock for more than one year and short-term if held one year or less.

Tax Consequences to Us

There will be no tax consequences to us except that we will be entitled to a deduction when a participant recognizes compensation income upon a disqualifying disposition. Any such deduction will be subject to the limitations of Section 162(m) of the Code.

Table of Contents

PROPOSAL 4: RATIFICATION OF SELECTION OF

Table of Contents

Our Audit Committee determined that the provision of the non-audit services by Ernst & Young LLP described above is compatible with maintaining Ernst & Young LLP'sLLP’s independence.

Table of Contents

EXECUTIVE OFFICERS