La Jolla Pharmaceutical (LJPC) 8-K La Jolla Pharmaceutical Company Announces Proposed Underwritten Public Offering of Common Stock

Exhibit 23.1

CONSENT OF INDEPENDENT REGISTERED PUBLIC ACCOUNTING FIRM

We consent to the incorporation by reference in Registration Statements on Form S-3(Nos. 333-214721 and333-206855) andForm S-8(Nos. 333-214722 and333-207212) of La Jolla Pharmaceutical Company of our report dated February 23, 2017, relating to our audits of the consolidated financial statements and internal control over financial reporting, which appear in the Annual Report on Form10-K of La Jolla Pharmaceutical Company for the year ended December 31, 2016.

/s/ SQUAR MILNER LLP

San Diego, California

March 20, 2017