EXHIBIT 5.1

January 4, 2021

Prelude Therapeutics Incorporated

200 Powder Mill Road

Wilmington, Delaware 19803

Ladies and Gentlemen:

At your request, we have examined the Registration Statement on Form S-1 (the “Registration Statement”) initially filed by Prelude Therapeutics Incorporated, a Delaware corporation (the “Company”), with the Securities and Exchange Commission (the “Commission”) on or about January 4, 2021, in connection with the registration under the Securities Act of 1933, as amended (“Securities Act”), of an aggregate of 2,012,500 shares of the Company’s common stock (including up to 262,500 shares subject to the underwriters’ option to purchase additional shares) (the “Shares”), consisting of the Company’s voting common stock, par value $0.0001 per share (the “Common Stock”), and, to the extent Shares are purchased by certain existing stockholders of the Company, including by entities affiliated with certain of the Company’s directors, the Company’s non-voting common stock, par value $0.0001 per share (the “Non-Voting Common Stock”).

In connection with our opinion expressed below we have examined originals or copies of the underwriting agreement pursuant to which the Shares will be sold to the underwriters, the Registration Statement, the prospectus prepared in connection with the Registration Statement (the “Prospectus”), the Company’s Restated Certificate of Incorporation (the “Certificate”), and the Company’s Restated Bylaws (the “Bylaws”), certain minutes and consents of the Company’s board of directors (the “Board”) or a committee or committees thereof and the Company’s stockholders relating to the Registration Statement, the Certificate and the Bylaws, and such other agreements, documents, certificates and statements of the Company, its transfer agent and public or government officials, as we have deemed advisable, and have examined such questions of law as we have considered necessary. In giving our opinion, we have also relied upon a good standing certificate regarding the Company issued by the Delaware Secretary of State and a management certificate addressed to us and dated of even date herewith executed by the Company containing certain factual representations by the Company.

In our examination of documents for purposes of this opinion, we have assumed, and express no opinion as to, the genuineness of all signatures on original documents, the authenticity and completeness of all documents submitted to us as originals, the conformity to originals and completeness of all documents submitted to us as copies, the legal capacity of all persons or entities executing the same (other than the Company), the lack of any undisclosed termination, modification, waiver or amendment to any document reviewed by us.

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.

In connection with our opinion expressed below, we have assumed that, at or prior to the time of the delivery of any shares of Shares, the Registration Statement will have been declared effective under the Securities Act that the registration will apply to the offer and sale of such shares of Shares and will not have been modified or rescinded and that there will not have occurred any change in law affecting the validity of the issuance of such shares of Shares.

Based upon the foregoing, we are of the opinion that the up to 2,012,500 Shares that may be issued and sold by the Company, when issued, sold and delivered in the manner and for the consideration stated in the Registration Statement

and the Prospectus and in accordance with the resolutions adopted by the Board and to be adopted by the Pricing Committee of the Board, will be validly issued, fully paid and nonassessable.

We consent to the use of this opinion as an exhibit to the Registration Statement and further consent to all references to us, if any, in the Registration Statement, the Prospectus constituting a part thereof and any amendments thereto.

This opinion is intended solely for use in connection with issuance and sale of the Shares subject to the Registration Statement and is not to be relied upon for any other purpose. This opinion is rendered as of the date first written above and is based solely on our understanding of facts in existence as of such date after the aforementioned examination. In rendering the opinions above, we are opining only as to the specific legal issues expressly set forth therein, and no opinion shall be inferred as to any other matter or matters. We assume no obligation to advise you of any fact, circumstance, event or change in the law or the facts that may hereafter be brought to our attention whether or not such occurrence would affect or modify any of the opinions expressed herein.