Apellis Pharmaceuticals (APLS) S-3ASR Automatic shelf registration

Exhibit 23.1

Consent of Independent Registered Public Accounting Firm

We consent to the reference to our firm under the caption “Experts” in the Registration Statement on FormS-3 and related Prospectus of Apellis Pharmaceuticals, Inc. for the registration of debt securities, common stock, preferred stock, units, and warrants and to the incorporation by reference therein of our reports dated February 26, 2019, with respect to the consolidated financial statements of Apellis Pharmaceuticals, Inc., and the effectiveness of internal control over financial reporting of Apellis Pharmaceuticals, Inc., included in its Annual Report (Form10-K) for the year ended December 31, 2018, filed with the Securities and Exchange Commission.

/s/ Ernst & Young LLP

Boston, Massachusetts

January 7, 2020