EX-5.1

Exhibit 5.1

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Goodwin Procter LLP

The New York Times Building
620 Eighth Avenue
New York, NY 10018

goodwinlaw.com

+1 212 813 8800

January 10, 2025

Amylyx Pharmaceuticals, Inc.

43 Thorndike St.

Cambridge, Massachusetts 02141

Re: Securities Registered under Registration Statement on Form S-3

We have acted as counsel to you in connection with your filing of a Registration Statement on Form S-3 (File No. 333-270505) (as amended or supplemented, the “Registration Statement”) filed on March 13, 2023 with the Securities and Exchange Commission (the “Commission”) pursuant to the Securities Act of 1933, as amended (the “Securities Act”), relating to the registration of the offer by Amylyx Pharmaceuticals, Inc., a Delaware corporation (the “Company”), of any combination of securities of the types specified therein. Reference is made to our opinion letter dated March 13, 2023 and included as Exhibit 5.1 to the Registration Statement.

We are delivering this supplemental opinion letter in connection with the prospectus supplement (the “Prospectus Supplement”) filed on January 10, 2025 by the Company with the Commission pursuant to Rule 424 under the Securities Act. The Prospectus Supplement relates to the offering by the Company of up to 19,714,285 shares (the “Shares”) of the Company’s common stock, par value $0.0001 per share (the “Common Stock”) covered by the Registration Statement. The Shares include an over-allotment option granted to the underwriter of the offering to purchase 2,571,428 Shares. The Shares are being sold to the underwriter named in, and pursuant to, an underwriting agreement between the Company and such underwriter (the “Underwriting Agreement”).

We have reviewed such documents and made such examination of law as we have deemed appropriate to give the opinion set forth below. We have relied, without independent verification, on certificates of public officials and, as to matters of fact material to the opinion set forth below, on certificates of officers of the Company.

The opinion set forth below is limited to the Delaware General Corporation Law. Based on the foregoing, we are of the opinion that:

The Shares have been duly authorized and, when delivered and paid for in accordance with the terms of the Underwriting Agreement, will be validly issued, fully paid and non-assessable.

This opinion letter and the opinion it contains shall be interpreted in accordance with the Core Opinion Principles as published in 74 Business Lawyer 815 (Summer 2019).