Document:

EX-10.13

 Exhibit 10.13 

EMPLOYMENT AGREEMENT 

This Employment Agreement (“Agreement”) is made between Amylyx Pharmaceuticals, Inc., a Delaware corporation (the
“Company”), and Justin Klee (the “Executive”) and is effective as of the closing of the Company’s first underwritten public offering of its equity securities pursuant to an effective registration statement
under the Securities Act of 1933, as amended (the “Effective Date”). Except with respect to the Restrictive Covenants Agreement and the Equity Documents (each as defined below) and subject to Section 12, this Agreement
supersedes in all respects all prior agreements between the Executive and the Company regarding the subject matter herein, including without limitation (i) the employment agreement between the Executive and the Company dated August 1, 2015
and later amended February 19, 2021 (the “Prior Agreement”), and (ii) any other offer letter, employment agreement or severance agreement. 

WHEREAS, the Company desires to continue to employ the Executive and the Executive desires to continue to be employed by the Company on the
new terms and conditions contained herein. 
 NOW, THEREFORE, in consideration of the mutual covenants and agreements herein
contained and other good and valuable consideration, the receipt and sufficiency of which is hereby acknowledged, the parties agree as follows: 

1. Employment. 
 (a)
Term. The Company shall employ the Executive and the Executive shall be employed by the Company pursuant to this Agreement commencing as of the Effective Date and continuing until such employment is terminated in accordance with the
provisions hereof (the “Term”). The Executive’s employment with the Company shall continue to be “at will,” meaning that the Executive’s employment may be terminated by the Company or the Executive at any time
and for any reason subject to the terms of this Agreement. 
 (b) Position and Duties. The Executive shall serve as the Co-Chief Executive Officer (the “CEO”) of the Company and shall have such powers and duties as may from time to time be prescribed by the Board of Directors (the “Board”). In
addition, the Executive currently serves on the Company’s Board and shall continue to so serve for as long as the Executive remains the CEO, subject to the terms of any applicable governing documents or bylaws applicable to the Board;
provided that the Executive shall be deemed to have resigned from the Board and from any related positions upon ceasing to serve as CEO for any reason. The Executive shall devote the Executive’s full working time and efforts to the
business and affairs of the Company. Notwithstanding the foregoing, the Executive may serve on other boards of directors, with the approval of the Board, or engage in religious, charitable or other community activities as long as such services and
activities do not interfere with the Executive’s performance of the Executive’s duties to the Company. 
 (c)
Location. The Executive’s primary work location will be in the Company’s office, currently located in Cambridge, Massachusetts; provided that the Executive may be required to travel regularly for business, consistent with the
Company’s business needs. 

 2. Compensation and Related Matters. 

(a) Base Salary. The Executive’s initial base salary shall be paid at the rate of $540,000 per year. The Executive’s base
salary shall be subject to periodic review by the Board or the Compensation Committee of the Board (the “Compensation Committee”). The base salary in effect at any given time is referred to herein as “Base
Salary.” The Base Salary shall be payable in a manner that is consistent with the Company’s usual payroll practices for its executive officers. 

(b) Incentive Compensation. The Executive shall be eligible to receive cash incentive compensation as determined by the Board or the
Compensation Committee from time to time. The Executive’s initial target annual incentive compensation shall be 60% of the Executive’s Base Salary. The target annual incentive compensation in effect at any given time is referred to herein
as “Target Bonus.” The actual amount of the Executive’s annual incentive compensation, if any, shall be determined in the sole discretion of the Board or the Compensation Committee. Any annual incentive compensation will be
paid no later than March 15th of the calendar year following the calendar year to which such bonus relates. Except as otherwise provided herein or as may be provided by the Board or the
Compensation Committee, the Executive must be employed by the Company on the date such incentive compensation is paid in order to earn or receive any annual incentive compensation. 

(c) Expenses. The Executive shall be entitled to receive prompt reimbursement for all reasonable expenses incurred by the Executive
during the Term in performing services hereunder, in accordance with the policies and procedures then in effect and established by the Company for its executive officers. 

(d) Other Benefits. The Executive shall be eligible to participate in or receive benefits under the Company’s employee benefit
plans in effect from time to time, subject to the terms of such plans. 
 (e) Paid Time Off. The Executive shall be entitled to take
paid time off in accordance with the Company’s applicable paid time off policy for executives, as may be in effect from time to time. 

(f) Equity. The equity awards held by the Executive shall continue to be governed by the terms and conditions of the Company’s
applicable equity incentive plan(s) and the applicable award agreement(s) governing the terms of such equity awards (collectively, the “Equity Documents”); provided, however, and notwithstanding anything to the contrary in
the Equity Documents, Section 5(b) of this Agreement shall apply in the event of a termination by the Company without Cause or by the Executive for Good Reason outside the Change in Control Period, Section 6 of this Agreement shall apply
in the event of a Change in Control and Section 7(a)(ii) of this Agreement shall apply in the event of a termination by the Company without Cause or by the Executive for Good Reason in either event within the Change in Control Period (as such
terms are defined below). 
 3. Termination. The Executive’s employment hereunder may be terminated without any breach of this
Agreement under the following circumstances: 

  
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 (a) Death. The Executive’s employment hereunder shall terminate upon death. 

(b) Disability. The Company may terminate the Executive’s employment if the Executive is disabled and unable to perform or expected
to be unable to perform the essential functions of the Executive’s then existing position or positions under this Agreement with or without reasonable accommodation for a period of 180 days (which need not be consecutive) in any 12-month period. If any question shall arise as to whether during any period the Executive is disabled so as to be unable to perform the essential functions of the Executive’s then existing position or
positions with or without reasonable accommodation, the Executive may, and at the request of the Company shall, submit to the Company a certification in reasonable detail by a physician selected by the Company to whom the Executive or the
Executive’s guardian has no reasonable objection as to whether the Executive is so disabled or how long such disability is expected to continue, and such certification shall for the purposes of this Agreement be conclusive of the issue. The
Executive shall cooperate with any reasonable request of the physician in connection with such certification. If such question shall arise and the Executive shall fail to submit such certification, the Company’s determination of such issue
shall be binding on the Executive. Nothing in this Section 3(b) shall be construed to waive the Executive’s rights, if any, under existing law including, without limitation, the Family and Medical Leave Act of 1993, 29 U.S.C. §2601
et seq. and the Americans with Disabilities Act, 42 U.S.C. §12101 et seq. 
 (c) Termination by the Company for
Cause. The Company may terminate the Executive’s employment hereunder for Cause. For purposes of this Agreement, “Cause” shall mean any of the following: 

(i) conduct by the Executive constituting a material act of misconduct in connection with the performance of the Executive’s duties,
including, without limitation, (A) willful failure or refusal to perform material responsibilities that have been requested by the Board; (B) dishonesty to the Board with respect to any material matter; or (C) misappropriation of
funds or property of the Company or any of its subsidiaries or affiliates other than the occasional, customary and de minimis use of Company property for personal purposes; 

(ii) the commission by the Executive of acts satisfying the elements of (A) any felony or (B) a misdemeanor involving moral
turpitude, deceit, dishonesty or fraud; 
 (iii) any misconduct by the Executive, regardless of whether or not in the course of the
Executive’s employment, that would reasonably be expected to result in material injury or reputational harm to the Company or any of its subsidiaries or affiliates if the Executive were to continue to be employed in the same position; 

(iv) continued unsatisfactory performance or non-performance by the Executive of the Executive’s
duties hereunder (other than by reason of the Executive’s physical or mental illness, incapacity or disability) which has continued for more than 30 days following written notice of such unsatisfactory performance or non-performance from the Board; 

  
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 (v) a breach by the Executive of any of the provisions contained in Section 9 of this
Agreement or the Restrictive Covenants Agreement; 
 (vi) a material violation by the Executive of any of the Company’s written
employment policies; or 
 (vii) the Executive’s failure to cooperate with a bona fide internal investigation or an investigation by
regulatory or law enforcement authorities, after being instructed by the Company to cooperate, or the willful destruction or failure to preserve documents or other materials known to be relevant to such investigation or the inducement of others to
fail to cooperate or to produce documents or other materials in connection with such investigation. 
 (d) Termination by the Company
without Cause. The Company may terminate the Executive’s employment hereunder at any time without Cause. Any termination by the Company of the Executive’s employment under this Agreement which does not constitute a termination for
Cause under Section 3(c) and does not result from the death or disability of the Executive under Section 3(a) or (b) shall be deemed a termination without Cause. 

(e) Termination by the Executive. The Executive may terminate employment hereunder at any time for any reason, including but not limited
to, Good Reason. For purposes of this Agreement, “Good Reason” shall mean that the Executive has completed all steps of the Good Reason Process (hereinafter defined) following the occurrence of any of the following events without
the Executive’s consent (each, a “Good Reason Condition”): 
 (i) a material diminution in the Executive’s
responsibilities, authority or duties; 
 (ii) a material diminution in the Executive’s Base Salary except for across-the-board salary reductions based on the Company’s financial performance similarly affecting all or substantially all senior management employees of the Company;

 (iii) a material change in the geographic location of the principal office of the Company to which the Executive is assigned, such that
there is an increase of at least thirty (30) miles of driving distance to such location from the Executive’s principal residence as of such change; or 

(iv) a material breach of this Agreement by the Company. 

The “Good Reason Process” consists of the following steps: 

(i) the Executive reasonably determines in good faith that a Good Reason Condition has occurred; 

(ii) the Executive notifies the Company in writing of the first occurrence of the Good Reason Condition within 60 days of the first occurrence
of such condition; 

  
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 (iii) the Executive cooperates in good faith with the Company’s efforts, for a period
of not less than 30 days following such notice (the “Cure Period”), to remedy the Good Reason Condition; 
 (iv)
notwithstanding such efforts, the Good Reason Condition continues to exist at the end of the Cure Period; and 
 (v) the Executive
terminates employment within 60 days after the end of the Cure Period. 
 If the Company cures the Good Reason Condition during the Cure Period, Good Reason
shall be deemed not to have occurred. 
 4. Matters Related to Termination. 

(a) Notice of Termination. Except for termination as specified in Section 3(a), any termination of the Executive’s employment
by the Company or any such termination by the Executive shall be communicated by written Notice of Termination to the other party hereto. For purposes of this Agreement, a “Notice of Termination” shall mean a notice which shall
indicate the specific termination provision in this Agreement relied upon. 
 (b) Date of Termination. “Date of
Termination” shall mean: (i) if the Executive’s employment is terminated by death, the date of death; (ii) if the Executive’s employment is terminated on account of disability under Section 3(b) or by the Company
for Cause under Section 3(c), the date on which Notice of Termination is given; (iii) if the Executive’s employment is terminated by the Company without Cause under Section 3(d), the date on which a Notice of Termination is given
or the date otherwise specified by the Company in the Notice of Termination; (iv) if the Executive’s employment is terminated by the Executive under Section 3(e) other than for Good Reason, 30 days after the date on which a Notice of
Termination is given, and (v) if the Executive’s employment is terminated by the Executive under Section 3(e) for Good Reason, the date on which a Notice of Termination is given after the end of the Cure Period. Notwithstanding the
foregoing, in the event that the Executive gives a Notice of Termination to the Company, the Company may unilaterally accelerate the Date of Termination and such acceleration shall not result in a termination by the Company for purposes of this
Agreement. 
 (c) Accrued Obligations. If the Executive’s employment with the Company is terminated for any reason, the Company
shall pay or provide to the Executive (or to the Executive’s authorized representative or estate) (i) any Base Salary earned through the Date of Termination; (ii) unpaid expense reimbursements (subject to, and in accordance
with, Section 2(c) of this Agreement); and (iii) any vested benefits the Executive may have under any employee benefit plan of the Company through the Date of Termination, which vested benefits shall be paid and/or provided in accordance
with the terms of such employee benefit plans (collectively, the “Accrued Obligations”). 
 (d) Resignation of All Other
Positions. To the extent applicable, the Executive shall be deemed to have resigned from all officer and board member positions that the Executive holds with the Company or any of its respective subsidiaries and affiliates upon the termination
of the Executive’s employment for any reason. The Executive shall execute any documents in reasonable form as may be requested to confirm or effectuate any such resignations. 

  
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 5. Severance Pay and Benefits Upon Termination by the Company without Cause or by the
Executive for Good Reason Outside the Change in Control Period. If the Executive’s employment is terminated by the Company without Cause as provided in Section 3(d), or the Executive terminates employment for Good Reason as provided in
Section 3(e), in each case outside of the Change in Control Period, then, in addition to the Accrued Obligations, and subject to (i) the Executive signing a separation agreement and release in a form and manner satisfactory to the
Company, which shall include, without limitation, a general release of claims against the Company and all related persons and entities that shall not release the Executive’s rights under this Agreement, a reaffirmation of all of the
Executive’s Continuing Obligations (as defined below), and, in the Company’s sole discretion, a one-year post-employment noncompetition agreement, and shall provide that if the Executive breaches any
of the Continuing Obligations, all payments of the Severance Amount shall immediately cease (the “Separation Agreement”), and (ii) the Separation Agreement becoming irrevocable, all within 60 days after the Date of Termination
(or such shorter period as set forth in the Separation Agreement), which shall include a seven (7) business day revocation period: 

(a) the Company shall pay the Executive an amount equal to the sum of (i) 12 months of the Executive’s Base Salary plus (ii) a pro-rata portion of the Target Bonus (pursuant to Section 2(b)) for the calendar year in which the Date of Termination occurs based on the number of days the Executive was employed by the Company in such
calendar year (the “Severance Amount”); and 
 (b) notwithstanding anything to the contrary in any applicable option
agreement or other stock-based award agreement, the stock options and other stock-based awards held by the Executive that are solely subject to time-based vesting (“Time-Based Equity Awards”) and that would have become fully vested
and exercisable or nonforfeitable had the Executive remained employed by the Company for the 12-month period immediately following the Date of Termination, shall immediately accelerate and become fully vested
and exercisable or nonforfeitable as of the later of (i) the Date of Termination or (ii) the effective date of the Release (the “Accelerated Vesting Date”), provided that in order to effectuate the accelerated
vesting contemplated by this subsection, the unvested portion of the Executive’s Time-Based Equity Awards that would otherwise be forfeited on the Date of Termination will be delayed until the earlier of (A) the effective date of the
Release (at which time acceleration will occur), or (B) the date that the Release can no longer become fully effective (at which time the unvested portion of the Executive’s Time-Based Equity Awards will be forfeited). Notwithstanding the
foregoing, no additional time-based vesting of the Time-Based Equity Awards shall occur during the period between the Date of Termination and the Accelerated Vesting Date; and 

  
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 (c) subject to the Executive’s copayment of premium amounts at the applicable active
employees’ rate and the Executive’s proper election to receive benefits under the Consolidated Omnibus Budget Reconciliation Act of 1985, as amended (“COBRA”), the Company shall pay to the group health plan provider or the
COBRA provider a monthly payment equal to the monthly employer contribution that the Company would have made to provide health insurance to the Executive if the Executive had remained employed by the Company until the earliest of (i) the 12-month anniversary of the Date of Termination; (ii) the date that the Executive becomes eligible for group medical plan benefits under any other employer’s group medical plan; or (iii) the cessation
of the Executive’s health continuation rights under COBRA; provided, however, that if the Company determines that it cannot pay such amounts to the group health plan provider or the COBRA provider (if applicable) without potentially
violating applicable law (including, without limitation, Section 2716 of the Public Health Service Act), then the Company shall convert such payments to payroll payments directly to the Executive for the time period specified above. Such
payments to the Executive shall be subject to tax-related deductions and withholdings and paid on the Company’s regular payroll dates. 

The amounts payable under Section 5, to the extent taxable, shall be paid out in substantially equal installments in accordance with the Company’s
payroll practice over 12 months commencing within 60 days after the Date of Termination; provided, however, that if the 60-day period begins in one calendar year and ends in a second calendar
year, such payments, to the extent they qualify as “non-qualified deferred compensation” within the meaning of Section 409A of the Internal Revenue Code of 1986, as amended (the
“Code”), shall begin to be paid in the second calendar year by the last day of such 60-day period; provided, further, that the initial payment shall include a catch-up payment to cover amounts retroactive to the day immediately following the Date of Termination. Each payment pursuant to this Agreement is intended to constitute a separate payment for purposes of Treasury
Regulation Section 1.409A-2(b)(2). 
 6. Change in Control. Upon a Change in Control,
except as otherwise explicitly set forth in the applicable equity award agreement, any stock options and other stock-based awards held by the Executive with conditions and restrictions relating to the attainment of performance goals
(“Performance-Based Equity Awards”), to the extent then outstanding and unearned, shall be deemed earned based on the greater of target or actual performance as measured through such Change in Control, and such Performance-Based
Equity Awards that are deemed earned shall be subject to time-based vesting, based on Executive’s continued employment, for the remainder of the performance period and shall be subject to accelerated vesting upon a termination of
Executive’s employment to the extent provided for in Section 7(a)(ii) below. Any Performance-Based Equity Awards that are not deemed earned upon a Change in Control shall be forfeited for no consideration upon such Change in Control. 

7. Severance Pay and Benefits Upon Termination by the Company without Cause or by the Executive for Good Reason within the Change in Control
Period. The provisions of this Section 7 shall apply in lieu of, and expressly supersede, the provisions of Section 5 if (i) the Executive’s employment is terminated either (a) by the Company without Cause as provided in
Section 3(d), or (b) by the Executive for Good Reason as provided in Section 3(e), and (ii) the Date of Termination is on or within three (3) months prior to or 12 months after the occurrence of the first event constituting
a Change in Control (such period, the “Change in Control Period”). These provisions shall terminate and be of no further force or effect after the Change in Control Period. 

  
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 (a) If the Executive’s employment is terminated by the Company without Cause as
provided in Section 3(d) or the Executive terminates employment for Good Reason as provided in Section 3(e) and in each case the Date of Termination occurs during the Change in Control Period, then, in addition to the Accrued Obligations,
and subject to the signing of a general release of claims against the Company and all related persons and entities that shall not release the Executive’s rights under this Agreement (the “Release”) by the Executive and the
Release becoming fully effective, all within the time frame set forth in the Release but in no event more than 60 days after the Date of Termination: 

(i) the Company shall pay the Executive a lump sum in cash in an amount equal to 1.5 times the sum of (A) the Executive’s
then-current Base Salary (or the Executive’s Base Salary in effect immediately prior to the Change in Control, if higher) plus (B) the Executive’s Target Bonus for the then-current year (or the Executive’s Target Bonus in effect
immediately prior to the Change in Control, if higher) (the “Change in Control Payment”); and 
 (ii) notwithstanding
anything to the contrary in any applicable option agreement or other stock-based award agreement, all Time-Based Equity Awards and any Performance-Based Equity Awards that are then outstanding and eligible to vest based on Executive’s continued
employment as provided for under Section 6 above shall immediately accelerate and become fully vested and exercisable or nonforfeitable as of the Accelerated Vesting Date, provided that in order to effectuate the accelerated vesting
contemplated by this subsection, the unvested portion of the Executive’s Time-Based Equity Awards and Performance-Based Equity Awards that would otherwise be forfeited on the Date of Termination will be delayed until the earlier of (A) the
effective date of the Release (at which time acceleration will occur), or (B) the date that the Release can no longer become fully effective (at which time the unvested portion of the Executive’s Time-Based Equity Awards and
Performance-Based Equity Awards will be forfeited). Notwithstanding the foregoing, no additional time-based vesting of the Time-Based Equity Awards or Performance-Based Equity Awards shall occur during the period between the Date of Termination and
the Accelerated Vesting Date; and 
 (iii) subject to the Executive’s copayment of premium amounts at the applicable active
employees’ rate and the Executive’s proper election to receive benefits under COBRA, the Company shall pay to the group health plan provider or the COBRA provider a monthly payment equal to the monthly employer contribution that the
Company would have made to provide health insurance to the Executive if the Executive had remained employed by the Company until the earliest of (A) the 18-month anniversary of the Date of Termination;
(B) the date that the Executive becomes eligible for group medical plan benefits under any other employer’s group medical plan; or (C) the cessation of the Executive’s health continuation rights under COBRA; provided,
however, that if the Company determines that it cannot pay such amounts to the group health plan provider or the COBRA provider (if applicable) without potentially violating applicable law (including, without limitation, Section 2716 of the
Public Health Service Act), then the Company shall convert such payments to payroll payments directly to the Executive for the time period specified above. Such payments to the Executive shall be subject to
tax-related deductions and withholdings and paid on the Company’s regular payroll dates. 

  
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 The amounts payable under this Section 7(a), to the extent taxable, shall be paid or commence to be
paid within 60 days after the Date of Termination; provided, however, that if the 60-day period begins in one calendar year and ends in a second calendar year, such payments to the extent they qualify
as “non-qualified deferred compensation” within the meaning of Section 409A of the Code, shall be paid or commence to be paid in the second calendar year by the last day of such 60-day period. 
 (b) Additional Limitation. 

(i) Anything in this Agreement to the contrary notwithstanding, in the event that the amount of any compensation, payment or distribution by
the Company to or for the benefit of the Executive, whether paid or payable or distributed or distributable pursuant to the terms of this Agreement or otherwise, calculated in a manner consistent with Section 280G of the Code, and the
applicable regulations thereunder (the “Aggregate Payments”), would be subject to the excise tax imposed by Section 4999 of the Code, then the Aggregate Payments shall be reduced (but not below zero) so that the sum of all of
the Aggregate Payments shall be $1.00 less than the amount at which the Executive becomes subject to the excise tax imposed by Section 4999 of the Code; provided that such reduction shall only occur if it would result in the Executive
receiving a higher After Tax Amount (as defined below) than the Executive would receive if the Aggregate Payments were not subject to such reduction. In such event, the Aggregate Payments shall be reduced in the following order, in each case, in
reverse chronological order beginning with the Aggregate Payments that are to be paid the furthest in time from consummation of the transaction that is subject to Section 280G of the Code: (A) cash payments not subject to Section 409A
of the Code; (B) cash payments subject to Section 409A of the Code; (C) equity-based payments and acceleration; and (D) non-cash forms of benefits; provided that in the case of all
the foregoing Aggregate Payments all amounts or payments that are not subject to calculation under Treas. Reg. §1.280G-1, Q&A-24(b) or (c) shall be reduced
before any amounts that are subject to calculation under Treas. Reg. §1.280G-1, Q&A-24(b) or (c). 

(ii) For purposes of this Section 7(b), the “After Tax Amount” means the amount of the Aggregate Payments less all
federal, state, and local income, excise and employment taxes imposed on the Executive as a result of the Executive’s receipt of the Aggregate Payments. For purposes of determining the After Tax Amount, the Executive shall be deemed to pay
federal income taxes at the highest marginal rate of federal income taxation applicable to individuals for the calendar year in which the determination is to be made, and state and local income taxes at the highest marginal rates of individual
taxation in each applicable state and locality, net of the maximum reduction in federal income taxes which could be obtained from deduction of such state and local taxes. 

  
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 (iii) The determination as to whether a reduction in the Aggregate Payments shall be made
pursuant to Section 7(b)(i) shall be made by a nationally recognized accounting firm selected by the Company (the “Accounting Firm”), which shall provide detailed supporting calculations both to the Company and the Executive
within 15 business days of the Date of Termination, if applicable, or at such earlier time as is reasonably requested by the Company or the Executive. Any determination by the Accounting Firm shall be binding upon the Company and the Executive. 

(c) Definitions. For purposes of this Agreement, “Change in Control” shall have the meaning ascribed to the term
“Sale Event” as used in the Company’s 2022 Stock Option and Incentive Plan. 
 8. Section 409A. 

(a) Anything in this Agreement to the contrary notwithstanding, if at the time of the Executive’s separation from service within the
meaning of Section 409A of the Code, the Company determines that the Executive is a “specified employee” within the meaning of Section 409A(a)(2)(B)(i) of the Code, then to the extent any payment or benefit that the Executive
becomes entitled to under this Agreement or otherwise on account of the Executive’s separation from service would be considered deferred compensation otherwise subject to the 20 percent additional tax imposed pursuant to
Section 409A(a) of the Code as a result of the application of Section 409A(a)(2)(B)(i) of the Code, such payment shall not be payable and such benefit shall not be provided until the date that is the earlier of (i) six months and one
day after the Executive’s separation from service, or (ii) the Executive’s death. If any such delayed cash payment is otherwise payable on an installment basis, the first payment shall include a
catch-up payment covering amounts that would otherwise have been paid during the six-month period but for the application of this provision, and the balance of the
installments shall be payable in accordance with their original schedule. 
 (b) All in-kind benefits
provided and expenses eligible for reimbursement under this Agreement shall be provided by the Company or incurred by the Executive during the time periods set forth in this Agreement. All reimbursements shall be paid as soon as administratively
practicable, but in no event shall any reimbursement be paid after the last day of the taxable year following the taxable year in which the expense was incurred. The amount of in-kind benefits provided or
reimbursable expenses incurred in one taxable year shall not affect the in-kind benefits to be provided or the expenses eligible for reimbursement in any other taxable year (except for any lifetime or other
aggregate limitation applicable to medical expenses). Such right to reimbursement or in-kind benefits is not subject to liquidation or exchange for another benefit. 

(c) To the extent that any payment or benefit described in this Agreement constitutes
“non-qualified deferred compensation” under Section 409A of the Code, and to the extent that such payment or benefit is payable upon the Executive’s termination of employment, then such
payments or benefits shall be payable only upon the Executive’s “separation from service.” The determination of whether and when a separation from service has occurred shall be made in accordance with the presumptions set forth in
Treasury Regulation Section 1.409A-1(h). 

  
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 (d) The parties intend that this Agreement will be administered in accordance with
Section 409A of the Code. To the extent that any provision of this Agreement is ambiguous as to its compliance with Section 409A of the Code, the provision shall be read in such a manner so that all payments hereunder comply with
Section 409A of the Code. Each payment pursuant to this Agreement or the Restrictive Covenants Agreement is intended to constitute a separate payment for purposes of Treasury Regulation
Section 1.409A-2(b)(2). The parties agree that this Agreement may be amended, as reasonably requested by either party, and as may be necessary to fully comply with Section 409A of the Code and all
related rules and regulations in order to preserve the payments and benefits provided hereunder without additional cost to either party. 

(e) The Company makes no representation or warranty and shall have no liability to the Executive or any other person if any provisions of this
Agreement are determined to constitute deferred compensation subject to Section 409A of the Code but do not satisfy an exemption from, or the conditions of, such Section. 

9. Continuing Obligations.  

(a) Restrictive Covenants Agreement. In consideration for the increase of the Executive’s Base Salary and Target Bonus provided for
in this Agreement, such increases the Executive acknowledges the Executive would not otherwise be entitled to receive and are consideration that is fair and reasonable and independent of the Executive’s continued employment with the Company,
the Executive is required to enter into the Employee Confidentiality, Assignment and Nonsolicitation Agreement, attached hereto as Exhibit A (the “Restrictive Covenants Agreement”). For purposes of this Agreement, the
obligations in this Section 9, the obligations that arise in the Restrictive Covenants Agreement and the obligations that arise in Sections 6-8 of the Prior Agreement, and any other agreement relating to
confidentiality, assignment of inventions, or other restrictive covenants shall collectively be referred to as the “Continuing Obligations.” 

(b) Third-Party Agreements and Rights. The Executive hereby confirms that the Executive is not bound by the terms of any agreement with
any previous employer or other party which restricts in any way the Executive’s use or disclosure of information, other than confidentiality restrictions (if any), or the Executive’s engagement in any business. The Executive represents to
the Company that the Executive’s execution of this Agreement, the Executive’s employment with the Company and the performance of the Executive’s proposed duties for the Company will not violate any obligations the Executive may have
to any such previous employer or other party. In the Executive’s work for the Company, the Executive will not disclose or make use of any information in violation of any agreements with or rights of any such previous employer or other party,
and the Executive will not bring to the premises of the Company any copies or other tangible embodiments of non-public information belonging to or obtained from any such previous employment or other party.

  
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 (c) Litigation and Regulatory Cooperation. During and after the Executive’s
employment, the Executive shall cooperate fully with the Company in (i) the defense or prosecution of any claims or actions now in existence or which may be brought in the future against or on behalf of the Company which relate to events or
occurrences that transpired while the Executive was employed by the Company, and (ii) the investigation, whether internal or external, of any matters about which the Company believes the Executive may have knowledge or information. The
Executive’s full cooperation in connection with such claims, actions or investigations shall include, but not be limited to, being available to meet with counsel to answer questions or to prepare for discovery or trial and to act as a witness
on behalf of the Company at mutually convenient times. During and after the Executive’s employment, the Executive also shall cooperate fully with the Company in connection with any investigation or review of any federal, state or local
regulatory authority as any such investigation or review relates to events or occurrences that transpired while the Executive was employed by the Company. The Company shall reimburse the Executive for any reasonable out-of-pocket expenses incurred in connection with the Executive’s performance of obligations pursuant to this Section 9(c). 

(d) Relief. The Executive agrees that it would be difficult to measure any damages caused to the Company which might result from any
breach by the Executive of the Continuing Obligations, and that in any event money damages would be an inadequate remedy for any such breach. Accordingly, the Executive agrees that if the Executive breaches, or proposes to breach, any portion
of the Continuing Obligations, the Company shall be entitled, in addition to all other remedies that it may have, to an injunction or other appropriate equitable relief to restrain any such breach without showing or proving any actual damage to the
Company. 
 10. Consent to Jurisdiction. The parties hereby consent to the jurisdiction of the state and federal courts of the
Commonwealth of Massachusetts. Accordingly, with respect to any such court action, the Executive (a) submits to the exclusive personal jurisdiction of such courts; (b) consents to service of process; and (c) waives any other
requirement (whether imposed by statute, rule of court, or otherwise) with respect to personal jurisdiction or service of process. 
 11.
Waiver of Jury Trial. Each of the Executive and the Company irrevocably and unconditionally WAIVES ALL RIGHT TO TRIAL BY JURY IN ANY PROCEEDING (WHETHER BASED ON CONTRACT, TORT OR OTHERWISE) ARISING OUT OF OR RELATING TO THIS AGREEMENT OR THE
EXECUTIVE’S EMPLOYMENT BY THE COMPANY OR ANY AFFILIATE OF THE COMPANY, INCLUDING WITHOUT LIMITATION THE EXECUTIVE’S OR THE COMPANY’S PERFORMANCE UNDER, OR THE ENFORCEMENT OF, THIS AGREEMENT. 

12. Integration. This Agreement, together with the Restrictive Covenants Agreement and the certain Director and Officer
Indemnification Agreement to which the Executive and the Company are parties, constitutes the entire agreement between the parties with respect to the subject matter hereof and supersedes all prior agreements between the parties concerning such
subject matter, including the Prior Agreement, provided that Sections 6-8 of the Prior Agreement, the Equity Documents and any other agreement relating to confidentiality, assignment of inventions, or
other restrictive covenants shall remain in full force and effect. 
 13. Withholding; Tax Effect. All payments made by the Company to
the Executive under this Agreement shall be net of any tax or other amounts required to be withheld by the Company under applicable law. Nothing in this Agreement shall be construed to require the Company to make any payments to compensate the
Executive for any adverse tax effect associated with any payments or benefits or for any deduction or withholding from any payment or benefit. 

  
 12 

 14. Assignment; Successors and Assigns. Neither the Executive nor the Company may
make any assignment of this Agreement or any interest in it, by operation of law or otherwise, without the prior written consent of the other; provided, however, that the Company may assign its rights and obligations under this Agreement
(including the Restrictive Covenants Agreement) without the Executive’s consent to any affiliate or to any person or entity with whom the Company shall hereafter effect a reorganization or consolidation, into which the Company merges or to whom
it transfers all or substantially all of its properties or assets; provided, further that if the Executive remains employed or becomes employed by the Company, the purchaser or any of their affiliates in connection with any such transaction,
then the Executive shall not be entitled to any payments, benefits or vesting pursuant to Section 5 or Section 7 of this Agreement solely as a result of such transaction. This Agreement shall inure to the benefit of and be binding upon the
Executive and the Company, and each of the Executive’s and the Company’s respective successors, executors, administrators, heirs and permitted assigns. In the event of the Executive’s death after the Executive’s termination of
employment but prior to the completion by the Company of all payments due to the Executive under this Agreement, the Company shall continue such payments to the Executive’s beneficiary designated in writing to the Company prior to the
Executive’s death (or to the Executive’s estate, if the Executive fails to make such designation). 
 15. Enforceability. If
any portion or provision of this Agreement (including, without limitation, any portion or provision of any section of this Agreement) shall to any extent be declared illegal or unenforceable by a court of competent jurisdiction, then the remainder
of this Agreement, or the application of such portion or provision in circumstances other than those as to which it is so declared illegal or unenforceable, shall not be affected thereby, and each portion and provision of this Agreement shall be
valid and enforceable to the fullest extent permitted by law. 
 16. Survival. For the avoidance of doubt, the provisions of this
Agreement shall survive the termination of the Executive’s employment to the extent necessary to effectuate the terms contained herein. 

17. Waiver. No waiver of any provision hereof shall be effective unless made in writing and signed by the waiving party. The failure of
any party to require the performance of any term or obligation of this Agreement, or the waiver by any party of any breach of this Agreement, shall not prevent any subsequent enforcement of such term or obligation or be deemed a waiver of any
subsequent breach. 
 18. Notices. Any notices, requests, demands and other communications provided for by this Agreement shall be
sufficient if in writing and delivered in person or sent by a nationally recognized overnight courier service or by registered or certified mail, postage prepaid, return receipt requested, to the Executive at the last address the Executive has filed
in writing with the Company or, in the case of the Company, at its main offices, attention of the Board. 
 19. Amendment. This
Agreement may be amended or modified only by a written instrument signed by the Executive and by a duly authorized representative of the Company. 

  
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 20. Effect on Other Plans and Agreements. An election by the Executive to resign for
Good Reason under the provisions of this Agreement shall not be deemed a voluntary termination of employment by the Executive for the purpose of interpreting the provisions of any of the Company’s benefit plans, programs or policies. Nothing in
this Agreement shall be construed to limit the rights of the Executive under the Company’s benefit plans, programs or policies except as otherwise provided in Section 9 hereof, and except that the Executive shall have no rights to any
severance benefits under any Company severance pay plan, offer letter or otherwise. In the event that the Executive is party to an agreement with the Company providing for payments or benefits under such plan or agreement and under this Agreement,
the terms of this Agreement shall govern and the Executive may receive payment under this Agreement only and not both. Further, Section 5 and Section 7 of this Agreement are mutually exclusive and in no event shall the Executive be
entitled to payments or benefits pursuant to both Section 5 and Section 7 of this Agreement. 
 21. Governing Law. This is a
Massachusetts contract and shall be construed under and be governed in all respects by the laws of the Commonwealth of Massachusetts, without giving effect to the conflict of laws principles thereof. With respect to any disputes concerning federal
law, such disputes shall be determined in accordance with the law as it would be interpreted and applied by the United States Court of Appeals for the First Circuit. 

22. Counterparts. This Agreement may be executed in any number of counterparts, each of which when so executed and delivered shall be
taken to be an original; but such counterparts shall together constitute one and the same document. 
 [Signature page follows] 

  
 14 

 IN WITNESS WHEREOF, the parties have executed this Agreement effective on the Effective
Date. 
  

			
	AMYLYX PHARMACEUTICALS, INC.
		
	By:	 	
                     
               

	Its:	 	      

	
	EXECUTIVE
	
	      

	Justin KleeEX-10.14

 Exhibit 10.14 

EMPLOYMENT AGREEMENT 

This Employment Agreement (“Agreement”) is made between Amylyx Pharmaceuticals, Inc., a Delaware corporation (the
“Company”), and James Frates (the “Executive”) and is effective as of the closing of the Company’s first underwritten public offering of its equity securities pursuant to an effective registration statement
under the Securities Act of 1933, as amended (the “Effective Date”). Except with respect to the Restrictive Covenants Agreement and the Equity Documents (each as defined below) and subject to Section 12, this Agreement
supersedes in all respects all prior agreements between the Executive and the Company regarding the subject matter herein, including without limitation (i) the employment agreement between the Executive and the Company dated January 25,
2021 (the “Prior Agreement”), and (ii) any other offer letter, employment agreement or severance agreement. 

WHEREAS, the Company desires to continue to employ the Executive and the Executive desires to continue to be employed by the Company on the
new terms and conditions contained herein. 
 NOW, THEREFORE, in consideration of the mutual covenants and agreements herein
contained and other good and valuable consideration, the receipt and sufficiency of which is hereby acknowledged, the parties agree as follows: 

1. Employment. 
 (a)
Term. The Company shall employ the Executive and the Executive shall be employed by the Company pursuant to this Agreement commencing as of the Effective Date and continuing until such employment is terminated in accordance with the
provisions hereof (the “Term”). The Executive’s employment with the Company shall continue to be “at will,” meaning that the Executive’s employment may be terminated by the Company or the Executive at any time
and for any reason subject to the terms of this Agreement. 
 (b) Position and Duties. The Executive shall serve as the Chief
Financial Officer of the Company and shall have such powers and duties as may from time to time be prescribed by the Co-Chief Executive Officers (individually and collectively, the “CEO”) or
other duly authorized executive. The Executive shall devote the Executive’s full working time and efforts to the business and affairs of the Company. Notwithstanding the foregoing, the Executive may serve on other boards of directors, with the
approval of the Board of Directors of the Company (the “Board”), or engage in religious, charitable or other community activities as long as such services and activities do not interfere with the Executive’s performance of the
Executive’s duties to the Company. 
 (c) Location. The Executive’s primary work location will be in the
Company’s office, currently located in Cambridge, Massachusetts; provided that the Executive may be required to travel regularly for business, consistent with the Company’s business needs. 

 2. Compensation and Related Matters. 

(a) Base Salary. The Executive’s initial base salary shall be paid at the rate of $440,000 per year. The Executive’s base
salary shall be subject to periodic review by the Board or the Compensation Committee of the Board (the “Compensation Committee”). The base salary in effect at any given time is referred to herein as “Base
Salary.” The Base Salary shall be payable in a manner that is consistent with the Company’s usual payroll practices for its executive officers. 

(b) Incentive Compensation. The Executive shall be eligible to receive cash incentive compensation as determined by the Board or the
Compensation Committee from time to time. The Executive’s initial target annual incentive compensation shall be 40% of the Executive’s Base Salary. The target annual incentive compensation in effect at any given time is referred to herein
as “Target Bonus.” The actual amount of the Executive’s annual incentive compensation, if any, shall be determined in the sole discretion of the Board or the Compensation Committee. Any annual incentive compensation will be
paid no later than March 15th of the calendar year following the calendar year to which such bonus relates. Except as otherwise provided herein or as may be provided by the Board or the
Compensation Committee, the Executive must be employed by the Company on the date such incentive compensation is paid in order to earn or receive any annual incentive compensation. 

(c) Expenses. The Executive shall be entitled to receive prompt reimbursement for all reasonable expenses incurred by the Executive
during the Term in performing services hereunder, in accordance with the policies and procedures then in effect and established by the Company for its executive officers. 

(d) Other Benefits. The Executive shall be eligible to participate in or receive benefits under the Company’s employee benefit
plans in effect from time to time, subject to the terms of such plans. 
 (e) Paid Time Off. The Executive shall be entitled to take
paid time off in accordance with the Company’s applicable paid time off policy for executives, as may be in effect from time to time. 

(f) Equity. The equity awards held by the Executive shall continue to be governed by the terms and conditions of the Company’s
applicable equity incentive plan(s) and the applicable award agreement(s) governing the terms of such equity awards (collectively, the “Equity Documents”); provided, however, and notwithstanding anything to the contrary in
the Equity Documents, Section 6 of this Agreement shall apply in the event of a Change in Control and Section 7(a)(ii) of this Agreement shall apply in the event of a termination by the Company without Cause or by the Executive for Good
Reason in either event within the Change in Control Period (as such terms are defined below). 
 3. Termination. The Executive’s
employment hereunder may be terminated without any breach of this Agreement under the following circumstances: 
 (a) Death. The
Executive’s employment hereunder shall terminate upon death. 

  
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 (b) Disability. The Company may terminate the Executive’s employment if the
Executive is disabled and unable to perform or expected to be unable to perform the essential functions of the Executive’s then existing position or positions under this Agreement with or without reasonable accommodation for a period of 180
days (which need not be consecutive) in any 12-month period. If any question shall arise as to whether during any period the Executive is disabled so as to be unable to perform the essential functions of the
Executive’s then existing position or positions with or without reasonable accommodation, the Executive may, and at the request of the Company shall, submit to the Company a certification in reasonable detail by a physician selected by the
Company to whom the Executive or the Executive’s guardian has no reasonable objection as to whether the Executive is so disabled or how long such disability is expected to continue, and such certification shall for the purposes of this
Agreement be conclusive of the issue. The Executive shall cooperate with any reasonable request of the physician in connection with such certification. If such question shall arise and the Executive shall fail to submit such certification, the
Company’s determination of such issue shall be binding on the Executive. Nothing in this Section 3(b) shall be construed to waive the Executive’s rights, if any, under existing law including, without limitation, the Family and Medical
Leave Act of 1993, 29 U.S.C. §2601 et seq. and the Americans with Disabilities Act, 42 U.S.C. §12101 et seq. 
 (c)
Termination by the Company for Cause. The Company may terminate the Executive’s employment hereunder for Cause. For purposes of this Agreement, “Cause” shall mean any of the following: 

(i) conduct by the Executive constituting a material act of misconduct in connection with the performance of the Executive’s duties,
including, without limitation, (A) willful failure or refusal to perform material responsibilities that have been requested by the CEO; (B) dishonesty to the CEO with respect to any material matter; or (C) misappropriation of funds or
property of the Company or any of its subsidiaries or affiliates other than the occasional, customary and de minimis use of Company property for personal purposes; 

(ii) the commission by the Executive of acts satisfying the elements of (A) any felony or (B) a misdemeanor involving moral
turpitude, deceit, dishonesty or fraud; 
 (iii) any misconduct by the Executive, regardless of whether or not in the course of the
Executive’s employment, that would reasonably be expected to result in material injury or reputational harm to the Company or any of its subsidiaries or affiliates if the Executive were to continue to be employed in the same position; 

(iv) continued unsatisfactory performance or non-performance by the Executive of the Executive’s
duties hereunder (other than by reason of the Executive’s physical or mental illness, incapacity or disability) which has continued for more than 30 days following written notice of such unsatisfactory performance or non-performance from the CEO; 
 (v) a breach by the Executive of any of the provisions contained in
Section 9 of this Agreement or the Restrictive Covenants Agreement; 

  
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 (vi) a material violation by the Executive of any of the Company’s written employment
policies; or 
 (vii) the Executive’s failure to cooperate with a bona fide internal investigation or an investigation by regulatory or
law enforcement authorities, after being instructed by the Company to cooperate, or the willful destruction or failure to preserve documents or other materials known to be relevant to such investigation or the inducement of others to fail to
cooperate or to produce documents or other materials in connection with such investigation. 
 (d) Termination by the Company without
Cause. The Company may terminate the Executive’s employment hereunder at any time without Cause. Any termination by the Company of the Executive’s employment under this Agreement which does not constitute a termination for Cause under
Section 3(c) and does not result from the death or disability of the Executive under Section 3(a) or (b) shall be deemed a termination without Cause. 

(e) Termination by the Executive. The Executive may terminate employment hereunder at any time for any reason, including but not limited
to, Good Reason. For purposes of this Agreement, “Good Reason” shall mean that the Executive has completed all steps of the Good Reason Process (hereinafter defined) following the occurrence of any of the following events without
the Executive’s consent (each, a “Good Reason Condition”): 
 (i) a material diminution in the Executive’s
responsibilities, authority or duties; 
 (ii) a material diminution in the Executive’s Base Salary except for across-the-board salary reductions based on the Company’s financial performance similarly affecting all or substantially all senior management employees of the Company;

 (iii) a material change in the geographic location of the principal office of the Company to which the Executive is assigned, such that
there is an increase of at least thirty (30) miles of driving distance to such location from the Executive’s principal residence as of such change; or 

(iv) a material breach of this Agreement by the Company. 

The “Good Reason Process” consists of the following steps: 

(i) the Executive reasonably determines in good faith that a Good Reason Condition has occurred; 

(ii) the Executive notifies the Company in writing of the first occurrence of the Good Reason Condition within 60 days of the first occurrence
of such condition; 
 (iii) the Executive cooperates in good faith with the Company’s efforts, for a period of not less than 30 days
following such notice (the “Cure Period”), to remedy the Good Reason Condition; 

  
 4 

 (iv) notwithstanding such efforts, the Good Reason Condition continues to exist at the end
of the Cure Period; and 
 (v) the Executive terminates employment within 60 days after the end of the Cure Period. 

If the Company cures the Good Reason Condition during the Cure Period, Good Reason shall be deemed not to have occurred. 

4. Matters Related to Termination. 

(a) Notice of Termination. Except for termination as specified in Section 3(a), any termination of the Executive’s employment
by the Company or any such termination by the Executive shall be communicated by written Notice of Termination to the other party hereto. For purposes of this Agreement, a “Notice of Termination” shall mean a notice which shall
indicate the specific termination provision in this Agreement relied upon. 
 (b) Date of Termination. “Date of
Termination” shall mean: (i) if the Executive’s employment is terminated by death, the date of death; (ii) if the Executive’s employment is terminated on account of disability under Section 3(b) or by the Company
for Cause under Section 3(c), the date on which Notice of Termination is given; (iii) if the Executive’s employment is terminated by the Company without Cause under Section 3(d), the date on which a Notice of Termination is given
or the date otherwise specified by the Company in the Notice of Termination; (iv) if the Executive’s employment is terminated by the Executive under Section 3(e) other than for Good Reason, 30 days after the date on which a Notice of
Termination is given, and (v) if the Executive’s employment is terminated by the Executive under Section 3(e) for Good Reason, the date on which a Notice of Termination is given after the end of the Cure Period. Notwithstanding the
foregoing, in the event that the Executive gives a Notice of Termination to the Company, the Company may unilaterally accelerate the Date of Termination and such acceleration shall not result in a termination by the Company for purposes of this
Agreement. 
 (c) Accrued Obligations. If the Executive’s employment with the Company is terminated for any reason, the Company
shall pay or provide to the Executive (or to the Executive’s authorized representative or estate) (i) any Base Salary earned through the Date of Termination; (ii) unpaid expense reimbursements (subject to, and in accordance
with, Section 2(c) of this Agreement); and (iii) any vested benefits the Executive may have under any employee benefit plan of the Company through the Date of Termination, which vested benefits shall be paid and/or provided in accordance
with the terms of such employee benefit plans (collectively, the “Accrued Obligations”). 
 (d) Resignation of All Other
Positions. To the extent applicable, the Executive shall be deemed to have resigned from all officer and board member positions that the Executive holds with the Company or any of its respective subsidiaries and affiliates upon the termination
of the Executive’s employment for any reason. The Executive shall execute any documents in reasonable form as may be requested to confirm or effectuate any such resignations. 

  
 5 

 5. Severance Pay and Benefits Upon Termination by the Company without Cause or by the
Executive for Good Reason Outside the Change in Control Period. If the Executive’s employment is terminated by the Company without Cause as provided in Section 3(d), or the Executive terminates employment for Good Reason as provided in
Section 3(e), in each case outside of the Change in Control Period, then, in addition to the Accrued Obligations, and subject to (i) the Executive signing a separation agreement and release in a form and manner satisfactory to the
Company, which shall include, without limitation, a general release of claims against the Company and all related persons and entities that shall not release the Executive’s rights under this Agreement, a reaffirmation of all of the
Executive’s Continuing Obligations (as defined below), and, in the Company’s sole discretion, a one-year post-employment noncompetition agreement, and shall provide that if the Executive breaches any
of the Continuing Obligations, all payments of the Severance Amount shall immediately cease (the “Separation Agreement”), and (ii) the Separation Agreement becoming irrevocable, all within 60 days after the Date of Termination
(or such shorter period as set forth in the Separation Agreement), which shall include a seven (7) business day revocation period: 

(a) the Company shall pay the Executive an amount equal to nine (9) months of the Executive’s Base Salary (the “Severance
Amount”); and 
 (b) subject to the Executive’s copayment of premium amounts at the applicable active employees’ rate and
the Executive’s proper election to receive benefits under the Consolidated Omnibus Budget Reconciliation Act of 1985, as amended (“COBRA”), the Company shall pay to the group health plan provider or the COBRA provider a monthly
payment equal to the monthly employer contribution that the Company would have made to provide health insurance to the Executive if the Executive had remained employed by the Company until the earliest of (i) the nine (9) month anniversary
of the Date of Termination; (ii) the date that the Executive becomes eligible for group medical plan benefits under any other employer’s group medical plan; or (iii) the cessation of the Executive’s health continuation rights
under COBRA; provided, however, that if the Company determines that it cannot pay such amounts to the group health plan provider or the COBRA provider (if applicable) without potentially violating applicable law (including, without
limitation, Section 2716 of the Public Health Service Act), then the Company shall convert such payments to payroll payments directly to the Executive for the time period specified above. Such payments to the Executive shall be subject to tax-related deductions and withholdings and paid on the Company’s regular payroll dates. 
 The amounts payable under
Section 5, to the extent taxable, shall be paid out in substantially equal installments in accordance with the Company’s payroll practice over nine (9) months commencing within 60 days after the Date of Termination;
provided, however, that if the 60-day period begins in one calendar year and ends in a second calendar year, such payments, to the extent they qualify as
“non-qualified deferred compensation” within the meaning of Section 409A of the Internal Revenue Code of 1986, as amended (the “Code”), shall begin to be paid in the second
calendar year by the last day of such 60-day period; provided, further, that the initial payment shall include a catch-up payment to cover amounts retroactive to
the day immediately following the Date of Termination. Each payment pursuant to this Agreement is intended to constitute a separate payment for purposes of Treasury Regulation Section 1.409A-2(b)(2). 

  
 6 

 6. Change in Control. Upon a Change in Control, except as otherwise explicitly set
forth in the applicable equity award agreement, any stock options and other stock-based awards held by the Executive with conditions and restrictions relating to the attainment of performance goals (“Performance-Based Equity
Awards”), to the extent then outstanding and unearned, shall be deemed earned based on the greater of target or actual performance as measured through such Change in Control, and such Performance-Based Equity Awards that are deemed earned
shall be subject to time-based vesting, based on Executive’s continued employment, for the remainder of the performance period and shall be subject to accelerated vesting upon a termination of Executive’s employment to the extent provided
for in Section 7(a)(ii) below. Any Performance-Based Equity Awards that are not deemed earned upon a Change in Control shall be forfeited for no consideration upon such Change in Control. 

7. Severance Pay and Benefits Upon Termination by the Company without Cause or by the Executive for Good Reason within the Change in Control
Period. The provisions of this Section 7 shall apply in lieu of, and expressly supersede, the provisions of Section 5 if (i) the Executive’s employment is terminated either (a) by the Company without Cause as provided in
Section 3(d), or (b) by the Executive for Good Reason as provided in Section 3(e), and (ii) the Date of Termination is on or within three (3) months prior to or 12 months after the occurrence of the first event constituting
a Change in Control (such period, the “Change in Control Period”). These provisions shall terminate and be of no further force or effect after the Change in Control Period. 

(a) If the Executive’s employment is terminated by the Company without Cause as provided in Section 3(d) or the Executive terminates
employment for Good Reason as provided in Section 3(e) and in each case the Date of Termination occurs during the Change in Control Period, then, in addition to the Accrued Obligations, and subject to the signing of a general release of claims
against the Company and all related persons and entities that shall not release the Executive’s rights under this Agreement (the “Release”) by the Executive and the Release becoming fully effective, all within the time frame
set forth in the Release but in no event more than 60 days after the Date of Termination: 
 (i) the Company shall pay the Executive a lump
sum in cash in an amount equal to 1.0 times the sum of (A) the Executive’s then-current Base Salary (or the Executive’s Base Salary in effect immediately prior to the Change in Control, if higher) plus (B) the Executive’s
Target Bonus for the then-current year (or the Executive’s Target Bonus in effect immediately prior to the Change in Control, if higher) (the “Change in Control Payment”); and 

  
 7 

 (ii) notwithstanding anything to the contrary in any applicable option agreement or other
stock-based award agreement, all stock options and other stock-based awards held by the Executive that are subject solely to time-based vesting ( “Time-Based Equity Awards”) and any Performance-Based Equity Awards that are then
outstanding and eligible to vest based on Executive’s continued employment as provided for under Section 6 above shall immediately accelerate and become fully vested and exercisable or nonforfeitable as of the later of (i) the
Date of Termination or (ii) the effective date of the Release (the “Accelerated Vesting Date”), provided that in order to effectuate the accelerated vesting contemplated by this subsection, the unvested portion of the
Executive’s Time-Based Equity Awards and Performance-Based Equity Awards that would otherwise be forfeited on the Date of Termination will be delayed until the earlier of (A) the effective date of the Release (at which time acceleration
will occur), or (B) the date that the Release can no longer become fully effective (at which time the unvested portion of the Executive’s Time-Based Equity Awards and Performance-Based Equity Awards will be forfeited). Notwithstanding the
foregoing, no additional time-based vesting of the Time-Based Equity Awards or Performance-Based Equity Awards shall occur during the period between the Date of Termination and the Accelerated Vesting Date; and 

(iii) subject to the Executive’s copayment of premium amounts at the applicable active employees’ rate and the Executive’s
proper election to receive benefits under COBRA, the Company shall pay to the group health plan provider or the COBRA provider a monthly payment equal to the monthly employer contribution that the Company would have made to provide health insurance
to the Executive if the Executive had remained employed by the Company until the earliest of (A) the 12-month anniversary of the Date of Termination; (B) the date that the Executive becomes eligible
for group medical plan benefits under any other employer’s group medical plan; or (C) the cessation of the Executive’s health continuation rights under COBRA; provided, however, that if the Company determines that it cannot pay
such amounts to the group health plan provider or the COBRA provider (if applicable) without potentially violating applicable law (including, without limitation, Section 2716 of the Public Health Service Act), then the Company shall convert
such payments to payroll payments directly to the Executive for the time period specified above. Such payments to the Executive shall be subject to tax-related deductions and withholdings and paid on the
Company’s regular payroll dates. 
 The amounts payable under this Section 7(a), to the extent taxable, shall be paid or commence to be paid
within 60 days after the Date of Termination; provided, however, that if the 60-day period begins in one calendar year and ends in a second calendar year, such payments to the extent they qualify as “non-qualified deferred compensation” within the meaning of Section 409A of the Code, shall be paid or commence to be paid in the second calendar year by the last day of such 60-day period. 
 (b) Additional Limitation. 

(i) Anything in this Agreement to the contrary notwithstanding, in the event that the amount of any compensation, payment or distribution by
the Company to or for the benefit of the Executive, whether paid or payable or distributed or distributable pursuant to the terms of this Agreement or otherwise, calculated in a manner consistent with Section 280G of the Code, and the
applicable regulations thereunder (the “Aggregate Payments”), would be subject to the excise tax imposed by Section 4999 of the Code, then the Aggregate Payments shall be reduced (but not below zero) so that the sum of all of
the Aggregate Payments shall be $1.00 less than the amount at which the Executive becomes subject to the excise tax imposed by Section 4999 of the Code; provided that such reduction shall only occur if it would result in the Executive
receiving a higher After Tax Amount (as defined below) than the Executive would receive if the Aggregate Payments were not subject to such reduction. In such event, the Aggregate Payments shall be reduced in the following order, in each case, in
reverse chronological order beginning with the Aggregate Payments that are to be paid the furthest in time from consummation of the transaction that is subject to Section 280G of the Code: (A) cash payments not subject to Section 409A
of the Code; (B) cash payments subject to Section 409A of the Code; (C) equity-based payments and acceleration; and (D) non-cash forms of benefits; provided that in the case of all
the foregoing Aggregate Payments all amounts or payments that are not subject to calculation under Treas. Reg. §1.280G-1, Q&A-24(b) or (c) shall be reduced
before any amounts that are subject to calculation under Treas. Reg. §1.280G-1, Q&A-24(b) or (c). 

  
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 (ii) For purposes of this Section 7(b), the “After Tax Amount” means
the amount of the Aggregate Payments less all federal, state, and local income, excise and employment taxes imposed on the Executive as a result of the Executive’s receipt of the Aggregate Payments. For purposes of determining the After Tax
Amount, the Executive shall be deemed to pay federal income taxes at the highest marginal rate of federal income taxation applicable to individuals for the calendar year in which the determination is to be made, and state and local income taxes at
the highest marginal rates of individual taxation in each applicable state and locality, net of the maximum reduction in federal income taxes which could be obtained from deduction of such state and local taxes. 

(iii) The determination as to whether a reduction in the Aggregate Payments shall be made pursuant to Section 7(b)(i) shall be made by a
nationally recognized accounting firm selected by the Company (the “Accounting Firm”), which shall provide detailed supporting calculations both to the Company and the Executive within 15 business days of the Date of Termination, if
applicable, or at such earlier time as is reasonably requested by the Company or the Executive. Any determination by the Accounting Firm shall be binding upon the Company and the Executive. 

(c) Definitions. For purposes of this Agreement, “Change in Control” shall have the meaning ascribed to the term
“Sale Event” as used in the Company’s 2022 Stock Option and Incentive Plan. 
 8. Section 409A. 

(a) Anything in this Agreement to the contrary notwithstanding, if at the time of the Executive’s separation from service within the
meaning of Section 409A of the Code, the Company determines that the Executive is a “specified employee” within the meaning of Section 409A(a)(2)(B)(i) of the Code, then to the extent any payment or benefit that the Executive
becomes entitled to under this Agreement or otherwise on account of the Executive’s separation from service would be considered deferred compensation otherwise subject to the 20 percent additional tax imposed pursuant to
Section 409A(a) of the Code as a result of the application of Section 409A(a)(2)(B)(i) of the Code, such payment shall not be payable and such benefit shall not be provided until the date that is the earlier of (i) six months and one
day after the Executive’s separation from service, or (ii) the Executive’s death. If any such delayed cash payment is otherwise payable on an installment basis, the first payment shall include a
catch-up payment covering amounts that would otherwise have been paid during the six-month period but for the application of this provision, and the balance of the
installments shall be payable in accordance with their original schedule. 

  
 9 

 (b) All in-kind benefits provided and expenses
eligible for reimbursement under this Agreement shall be provided by the Company or incurred by the Executive during the time periods set forth in this Agreement. All reimbursements shall be paid as soon as administratively practicable, but in no
event shall any reimbursement be paid after the last day of the taxable year following the taxable year in which the expense was incurred. The amount of in-kind benefits provided or reimbursable expenses
incurred in one taxable year shall not affect the in-kind benefits to be provided or the expenses eligible for reimbursement in any other taxable year (except for any lifetime or other aggregate limitation
applicable to medical expenses). Such right to reimbursement or in-kind benefits is not subject to liquidation or exchange for another benefit. 

(c) To the extent that any payment or benefit described in this Agreement constitutes
“non-qualified deferred compensation” under Section 409A of the Code, and to the extent that such payment or benefit is payable upon the Executive’s termination of employment, then such
payments or benefits shall be payable only upon the Executive’s “separation from service.” The determination of whether and when a separation from service has occurred shall be made in accordance with the presumptions set forth in
Treasury Regulation Section 1.409A-1(h). 
 (d) The parties intend that this Agreement will be
administered in accordance with Section 409A of the Code. To the extent that any provision of this Agreement is ambiguous as to its compliance with Section 409A of the Code, the provision shall be read in such a manner so that all payments
hereunder comply with Section 409A of the Code. Each payment pursuant to this Agreement or the Restrictive Covenants Agreement is intended to constitute a separate payment for purposes of Treasury Regulation
Section 1.409A-2(b)(2). The parties agree that this Agreement may be amended, as reasonably requested by either party, and as may be necessary to fully comply with Section 409A of the Code and all
related rules and regulations in order to preserve the payments and benefits provided hereunder without additional cost to either party. 

(e) The Company makes no representation or warranty and shall have no liability to the Executive or any other person if any provisions of this
Agreement are determined to constitute deferred compensation subject to Section 409A of the Code but do not satisfy an exemption from, or the conditions of, such Section. 

9. Continuing Obligations.  

(a) Restrictive Covenants Agreement. In consideration for the increase of the Executive’s Base Salary and Target Bonus provided for
in this Agreement, such increases the Executive acknowledges the Executive would not otherwise be entitled to receive and are consideration that is fair and reasonable and independent of the Executive’s continued employment with the Company,
the Executive is required to enter into the Employee Confidentiality, Assignment and Nonsolicitation Agreement, attached hereto as Exhibit A (the “Restrictive Covenants Agreement”). For purposes of this Agreement, the
obligations in this Section 9, the obligations that arise in the Restrictive Covenants Agreement and the obligations that arise in Sections 6-8 of the Prior Agreement, and any other agreement relating to
confidentiality, assignment of inventions, or other restrictive covenants shall collectively be referred to as the “Continuing Obligations.” 

  
 10 

 (b) Third-Party Agreements and Rights. The Executive hereby confirms that the
Executive is not bound by the terms of any agreement with any previous employer or other party which restricts in any way the Executive’s use or disclosure of information, other than confidentiality restrictions (if any), or the
Executive’s engagement in any business. The Executive represents to the Company that the Executive’s execution of this Agreement, the Executive’s employment with the Company and the performance of the Executive’s proposed duties
for the Company will not violate any obligations the Executive may have to any such previous employer or other party. In the Executive’s work for the Company, the Executive will not disclose or make use of any information in violation of any
agreements with or rights of any such previous employer or other party, and the Executive will not bring to the premises of the Company any copies or other tangible embodiments of non-public information
belonging to or obtained from any such previous employment or other party. 
 (c) Litigation and Regulatory Cooperation. During and
after the Executive’s employment, the Executive shall cooperate fully with the Company in (i) the defense or prosecution of any claims or actions now in existence or which may be brought in the future against or on behalf of the Company
which relate to events or occurrences that transpired while the Executive was employed by the Company, and (ii) the investigation, whether internal or external, of any matters about which the Company believes the Executive may have knowledge or
information. The Executive’s full cooperation in connection with such claims, actions or investigations shall include, but not be limited to, being available to meet with counsel to answer questions or to prepare for discovery or trial and to
act as a witness on behalf of the Company at mutually convenient times. During and after the Executive’s employment, the Executive also shall cooperate fully with the Company in connection with any investigation or review of any federal, state
or local regulatory authority as any such investigation or review relates to events or occurrences that transpired while the Executive was employed by the Company. The Company shall reimburse the Executive for any reasonable out-of-pocket expenses incurred in connection with the Executive’s performance of obligations pursuant to this Section 9(c). 

(d) Relief. The Executive agrees that it would be difficult to measure any damages caused to the Company which might result from any
breach by the Executive of the Continuing Obligations, and that in any event money damages would be an inadequate remedy for any such breach. Accordingly, the Executive agrees that if the Executive breaches, or proposes to breach, any portion
of the Continuing Obligations, the Company shall be entitled, in addition to all other remedies that it may have, to an injunction or other appropriate equitable relief to restrain any such breach without showing or proving any actual damage to the
Company. 
 10. Consent to Jurisdiction. The parties hereby consent to the jurisdiction of the state and federal courts of the
Commonwealth of Massachusetts. Accordingly, with respect to any such court action, the Executive (a) submits to the exclusive personal jurisdiction of such courts; (b) consents to service of process; and (c) waives any other
requirement (whether imposed by statute, rule of court, or otherwise) with respect to personal jurisdiction or service of process. 

  
 11 

 11. Waiver of Jury Trial. Each of the Executive and the Company irrevocably and
unconditionally WAIVES ALL RIGHT TO TRIAL BY JURY IN ANY PROCEEDING (WHETHER BASED ON CONTRACT, TORT OR OTHERWISE) ARISING OUT OF OR RELATING TO THIS AGREEMENT OR THE EXECUTIVE’S EMPLOYMENT BY THE COMPANY OR ANY AFFILIATE OF THE COMPANY,
INCLUDING WITHOUT LIMITATION THE EXECUTIVE’S OR THE COMPANY’S PERFORMANCE UNDER, OR THE ENFORCEMENT OF, THIS AGREEMENT. 
 12.
Integration. This Agreement, together with the Restrictive Covenants Agreement and the certain Officer Indemnification Agreement to which the Executive and the Company are parties, constitutes the entire agreement between the parties
with respect to the subject matter hereof and supersedes all prior agreements between the parties concerning such subject matter, including the Prior Agreement, provided that Sections 2(b) and 6-8 of
the Prior Agreement, the Equity Documents and any other agreement relating to confidentiality, assignment of inventions, or other restrictive covenants shall remain in full force and effect. 

13. Withholding; Tax Effect. All payments made by the Company to the Executive under this Agreement shall be net of any tax or other
amounts required to be withheld by the Company under applicable law. Nothing in this Agreement shall be construed to require the Company to make any payments to compensate the Executive for any adverse tax effect associated with any payments or
benefits or for any deduction or withholding from any payment or benefit. 
 14. Assignment; Successors and Assigns. Neither the
Executive nor the Company may make any assignment of this Agreement or any interest in it, by operation of law or otherwise, without the prior written consent of the other; provided, however, that the Company may assign its rights and
obligations under this Agreement (including the Restrictive Covenants Agreement) without the Executive’s consent to any affiliate or to any person or entity with whom the Company shall hereafter effect a reorganization or consolidation, into
which the Company merges or to whom it transfers all or substantially all of its properties or assets; provided, further that if the Executive remains employed or becomes employed by the Company, the purchaser or any of their affiliates in
connection with any such transaction, then the Executive shall not be entitled to any payments, benefits or vesting pursuant to Section 5 or Section 7 of this Agreement solely as a result of such transaction. This Agreement shall inure to
the benefit of and be binding upon the Executive and the Company, and each of the Executive’s and the Company’s respective successors, executors, administrators, heirs and permitted assigns. In the event of the Executive’s death after
the Executive’s termination of employment but prior to the completion by the Company of all payments due to the Executive under this Agreement, the Company shall continue such payments to the Executive’s beneficiary designated in writing
to the Company prior to the Executive’s death (or to the Executive’s estate, if the Executive fails to make such designation). 

15. Enforceability. If any portion or provision of this Agreement (including, without limitation, any portion or provision of any
section of this Agreement) shall to any extent be declared illegal or unenforceable by a court of competent jurisdiction, then the remainder of this Agreement, or the application of such portion or provision in circumstances other than those as to
which it is so declared illegal or unenforceable, shall not be affected thereby, and each portion and provision of this Agreement shall be valid and enforceable to the fullest extent permitted by law. 

  
 12 

 16. Survival. For the avoidance of doubt, the provisions of this Agreement shall
survive the termination of the Executive’s employment to the extent necessary to effectuate the terms contained herein. 
 17.
Waiver. No waiver of any provision hereof shall be effective unless made in writing and signed by the waiving party. The failure of any party to require the performance of any term or obligation of this Agreement, or the waiver by any party
of any breach of this Agreement, shall not prevent any subsequent enforcement of such term or obligation or be deemed a waiver of any subsequent breach. 

18. Notices. Any notices, requests, demands and other communications provided for by this Agreement shall be sufficient if in writing
and delivered in person or sent by a nationally recognized overnight courier service or by registered or certified mail, postage prepaid, return receipt requested, to the Executive at the last address the Executive has filed in writing with the
Company or, in the case of the Company, at its main offices, attention of the Board. 
 19. Amendment. This Agreement may be amended
or modified only by a written instrument signed by the Executive and by a duly authorized representative of the Company. 
 20. Effect on
Other Plans and Agreements. An election by the Executive to resign for Good Reason under the provisions of this Agreement shall not be deemed a voluntary termination of employment by the Executive for the purpose of interpreting the provisions
of any of the Company’s benefit plans, programs or policies. Nothing in this Agreement shall be construed to limit the rights of the Executive under the Company’s benefit plans, programs or policies except as otherwise provided in
Section 9 hereof, and except that the Executive shall have no rights to any severance benefits under any Company severance pay plan, offer letter or otherwise. In the event that the Executive is party to an agreement with the Company providing
for payments or benefits under such plan or agreement and under this Agreement, the terms of this Agreement shall govern and the Executive may receive payment under this Agreement only and not both. Further, Section 5 and Section 7 of this
Agreement are mutually exclusive and in no event shall the Executive be entitled to payments or benefits pursuant to both Section 5 and Section 7 of this Agreement. 

21. Governing Law. This is a Massachusetts contract and shall be construed under and be governed in all respects by the laws of the
Commonwealth of Massachusetts, without giving effect to the conflict of laws principles thereof. With respect to any disputes concerning federal law, such disputes shall be determined in accordance with the law as it would be interpreted and applied
by the United States Court of Appeals for the First Circuit. 
 22. Counterparts. This Agreement may be executed in any number of
counterparts, each of which when so executed and delivered shall be taken to be an original; but such counterparts shall together constitute one and the same document. 

[Signature page follows] 

  
 13 

 IN WITNESS WHEREOF, the parties have executed this Agreement effective on the Effective
Date. 
  

			
	AMYLYX PHARMACEUTICALS, INC.
		
	By:	 	
                     
           

	Its:	 	  

	
	EXECUTIVE
	
	  

	James Frates

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