Exhibit 31.2

CERTIFICATION OF CHIEF FINANCIAL OFFICER PURSUANT TO SECTION 302 OF THE SARBANES-OXLEY

ACT OF 2002

I, Ann D. Rhoads, certify that:

1. I have reviewed this Amendment No. 1 to the Quarterly Report on Form 10-Q of Zogenix, Inc.; and

2. Based on my knowledge, this report does not contain any untrue statement of a material fact or omit to state a material fact necessary to make the statements made, in light of the circumstances under which such statements were made, not misleading with respect to the period covered by this report.

/s/ Ann D. Rhoads

Ann D. Rhoads

Chief Financial Officer

Date: January 14, 2014