EX-5.1

Exhibit 5.1

February 15, 2024

Prelude Therapeutics Incorporated

175 Innovation Boulevard

Wilmington, Delaware 19805

Ladies and Gentlemen:

At your request, we have examined the Registration Statement on Form S-3 filed by Prelude Therapeutics Incorporated, a Delaware corporation (the “Company”), with the Securities and Exchange Commission (the “Commission”) on February 15, 2024 (the “Registration Statement”), in connection with the registration under the Securities Act of 1933, as amended (the “Securities Act”), of an aggregate of 7,936,759 shares of voting common stock, par value $0.0001 per share (the “Shares”), for offer and resale by the selling stockholders described and listed in the Registration Statement (the “Selling Stockholders”), consisting of 7,936,759 Shares issuable by the Company to the Selling Stockholders upon the exercise of a currently outstanding pre-funded warrants to purchase Shares issued by the Company to the Selling Stockholders.

In connection with our opinion expressed below, we have also examined originals or copies of the prospectus prepared in connection with the Registration Statement (the “Prospectus”); the Company’s current Amended and Restated Certificate of Incorporation and Amended and Restated Bylaws (collectively, the “Charter Documents”); the Amended and Restated Registration Rights Agreement, dated as of December 11, 2023, by and among the Company, 667, L.P, and Baker Brothers Life Sciences, L.P.; the Pre-Funded Warrants, dated December 13, 2023 by and among the Company, 667, L.P, and Baker Brothers Life Sciences, L.P. (the “Pre-Funded Warrant Agreements”); certain corporate proceedings of the Company’s board of directors and stockholders relating to the Registration Statement and the Charter Documents; and such other agreements, documents, certificates and statements of the Company, its transfer agent, its warrant agent and public or government officials, as we have deemed advisable, and have examined such questions of law as we have considered necessary. We have assumed the authenticity of all documents submitted to us as originals, the genuineness of all signatures on documents submitted to us, the conformity to originals of all documents submitted to us as copies, and the absence of any undisclosed termination, waiver or amendment to any document reviewed by us. In giving our opinion, we have also relied upon a good standing certificate issued by the Delaware Secretary of State and representations made to us by the Company, including representations that the Company has available a sufficient number of authorized Shares that are not currently outstanding or reserved for issuance under other outstanding securities or equity plans of the Company, to enable the Company to issue and deliver all of the Shares to be sold by the Selling Stockholders pursuant to the Registration Statement and the Prospectus.

We render this opinion only with respect to, and express no opinion herein concerning the application or effect of the laws of any jurisdiction other than, the existing Delaware General Corporation Law.

Based upon the foregoing, we are of the opinion that, the Shares that may be sold by the Selling Stockholders pursuant to the Registration Statement will, when delivered in the manner and for the consideration stated in the Registration Statement and the Prospectus, and when issued in accordance with the terms and conditions of the Pre-Funded Warrant Agreements, be validly issued, fully paid and nonassessable.