Waiver, dated as of August 5, 2019, to Amended and Restated Investors Rights Agreement, dated as of November 30, 2017, between Allakos Inc. and certain holders of the capital stock of Allakos Inc. named therein

Exhibit 4.1

EXECUTED VERSION

ALLAKOS INC.

WAIVER OF REGISTRATION RIGHTS

DATED AS OF AUGUST 5, 2019

Reference is hereby made to that certain Amended and Restated Investors’ Rights Agreement, dated as of November 30, 2017, as amended to date (the “Investors’ Rights Agreement”), by and among Allakos Inc., a Delaware corporation (the “Company”), and the Investors named therein (such Investors include each of the undersigned Holders of Registrable Securities). All capitalized terms used in this Waiver of Registration Rights (this “Waiver”) have the meanings ascribed to such terms in the Investors’ Rights Agreement unless otherwise defined herein. This Waiver shall be dated as of the date on which the Company or its agents receive the last signed counterpart signature page hereto necessary to give effect to the actions contemplated hereby.

WHEREAS: The Company is contemplating a potential public offering of the Company’s common stock, pursuant to an automatically effective registration statement on Form S-3 initially filed with the U.S. Securities and Exchange Commission on August 5, 2019, which is to be supplemented and completed on or before September 30, 2019 (the “Registered Offering”).

WHEREAS: Pursuant to, and subject to the terms and conditions of, Section 2.2 of the Investors’ Rights Agreement, if the Company proposes to register any of its stock or other securities under the Securities Act of 1933, as amended (the “Securities Act”), in connection with a public offering of securities, (x) the Company shall promptly give each Holder written notice of the proposed registration and (y) the Company shall use commercially reasonable efforts to include in such registration all Registrable Securities as are specified in a written request or requests made by any Holder or Holders received by the Company within ten (10) days of such written notice from the Company is mailed or delivered (the “Piggyback Registration Rights”).

WHEREAS: Pursuant to Section 5.1 of the Investors’ Rights Agreement, any term of the Investors’ Rights Agreement may be amended or waived with the written consent of (i) the Company and (ii) the Holders holding a majority of the Registrable Securities then outstanding, with such amendment or waiver to be binding on all current and future Holders of Registrable Securities.

NOW, THEREFORE, BE IT RESOLVED: Pursuant to Section 5.1 of the Investors’ Rights Agreement, the undersigned Holders of Registrable Securities, on their own behalf and on behalf of all current and future Holders of their respective Registrable Securities, hereby waive the Piggyback Registration Rights, and all notice and other rights related thereto, solely with respect to the Registered Offering.

[Signature page immediately follows]

This Waiver is hereby acknowledged and agreed on behalf of the undersigned:

[SIGNATURE PAGE TO WAIVER OF REGISTRATION RIGHTS]

This Waiver is hereby acknowledged and agreed on behalf of the undersigned:

[SIGNATURE PAGE TO WAIVER OF REGISTRATION RIGHTS]

This Waiver is hereby acknowledged and agreed on behalf of the undersigned:

[SIGNATURE PAGE TO WAIVER OF REGISTRATION RIGHTS]

This Waiver is hereby acknowledged and agreed on behalf of the undersigned:

[SIGNATURE PAGE TO WAIVER OF REGISTRATION RIGHTS]

This Waiver is hereby acknowledged and agreed on behalf of the undersigned:

[SIGNATURE PAGE TO WAIVER OF REGISTRATION RIGHTS]

This Waiver is hereby acknowledged and agreed on behalf of the undersigned:

[SIGNATURE PAGE TO WAIVER OF REGISTRATION RIGHTS]

This Waiver is hereby acknowledged and agreed on behalf of the undersigned:

[SIGNATURE PAGE TO WAIVER OF REGISTRATION RIGHTS]

This Waiver is hereby acknowledged and agreed on behalf of the undersigned:

[SIGNATURE PAGE TO WAIVER OF REGISTRATION RIGHTS]

This Waiver is hereby acknowledged and agreed on behalf of the undersigned:

[SIGNATURE PAGE TO WAIVER OF REGISTRATION RIGHTS]