Exhibit 99.1

Zogenix Provides Corporate Update and Reports

Third Quarter 2015 Financial Results

Company will host a conference call today at 4:30 p.m. EST/1:30 p.m. PST

SAN DIEGO, Calif., November 9, 2015 — Zogenix, Inc. (NASDAQ: ZGNX), a pharmaceutical company developing therapies for the treatment of central nervous system (CNS) disorders, provided a corporate update, and announced financial results for the third quarter ended September 30, 2015.

Corporate Update

“Over the past few months, we have made significant progress towards initiation of the Phase 3 program for ZX008 in the treatment of uncontrolled seizures in children with Dravet syndrome. While we are engaged in an ongoing information exchange with FDA to establish normal/abnormal values for interpretation of echocardiograms to be collected during the Phase 3 program, we continue to expect the U.S. pivotal efficacy and safety trial will proceed later this year,” said Stephen J. Farr, Ph.D., President and CEO. “We also continue to move ahead with Relday, having recently announced positive top-line pharmacokinetic results from a Phase 1b multi-dose clinical trial, and are actively seeking a global strategic development and commercialization partner for this program, which would represent another value creating event for Zogenix and the Company’s shareholders.”

Third Quarter 2015 Financial Results Compared to Third Quarter 2014 Financial Results

As a result of the sale of the Zohydro ER business, all Zohydro ER revenue and expenses have been excluded from continuing operations for all periods herein and reported as discontinued operations. All prior period information has been recast to conform to this presentation.

Nine-Months Ended September 30, 2015 Financial Results Compared to Nine-Months Ended September 30, 2014 Financial Results

As a result of the sale of the Zohydro ER business, all Zohydro ER revenue and expenses have been excluded from continuing operations for all periods herein and reported as discontinued operations. All prior period information has been recast to conform to this presentation.

2015 Financial Guidance

Below is the Company’s financial guidance for the remainder of 2015, which reflects spending towards the low end of the annual guidance ranges previously provided.

Additionally, the Company does not expect gain or loss from discontinued operations to be significant in the fourth quarter of 2015.

Conference Call Details

Investors interested in participating in today’s live call can dial 888-523-1228 from the U.S. and international callers can dial 719-325-2308 and use conference ID: 660434. A telephone replay will be available approximately two hours after the call and will run through November 23, 2015 by dialing 877-870-5176 from the U.S., or 858-384-5517 from international locations, and entering Replay Pin Number: 660434. The conference call will be broadcast live and will be available for replay for 60 days at: Conference Call Link and on the IR section of the company’s website at: Zogenix IR.

About Zogenix

Zogenix, Inc. (Nasdaq:ZGNX) is a pharmaceutical company committed to developing and commercializing CNS therapies that address specific clinical needs for people living with orphan and other CNS disorders who need innovative treatment alternatives to help them return to normal daily functioning.

Forward Looking Statements

Zogenix cautions you that statements included in this press release that are not a description of historical facts are forward-looking statements. Words such as “believes,” “anticipates,” “plans,” “expects,” “indicates,” “will,” “intends,” “potential,” “suggests,” “assuming,” “designed” and similar expressions are intended to identify forward-looking statements. These statements are based on the company’s current beliefs and expectations. These forward-looking statements include statements regarding: the Company’s financial guidance for the remainder of 2015; the Company’s cash position related to operating expenses and planned development activities; the timing of the commencement of Phase 3 clinical studies for ZX008; Zogenix’s strategy on advancing its novel pipeline in CNS disorders; and the expected timing of, and Zogenix’s ability to achieve, key clinical milestones and regulatory meetings and submissions for Zogenix’s development pipeline. The inclusion of forward-looking statements should not be regarded as a representation by Zogenix that any of its plans will be achieved. Actual results may differ from those set forth in this release due to the risks and uncertainties inherent in Zogenix’s business, including, without limitation: the uncertainties associated with the clinical development and regulatory approval of product candidates such as ZX008 and Relday, including potential delays in enrollment and completion of clinical trials; the potential that earlier clinical trials may not be predictive of future results; Zogenix’s reliance on third parties to conduct its clinical trials, enroll patients, manufacture its preclinical and clinical drug supplies and manufacture commercial supplies of its drug products, if approved; unexpected adverse side effects or inadequate therapeutic efficacy of ZX008 that could limit approval and/or commercialization, or that could result in recalls or product liability claims; Zogenix’s ability to fully comply with numerous federal, state and local laws and regulatory requirements that apply to its product development activities; Zogenix could spend its available financial resources faster than it currently expects and may be unable to raise additional capital if and when needed, on acceptable terms or at all; and other risks described in Zogenix’s prior press releases as well as in public periodic filings with the Securities and Exchange Commission. You are cautioned not to place undue reliance on these forward-looking statements, which speak only as of the date hereof, and Zogenix undertakes no obligation to revise or update this press release to reflect events or circumstances after the date hereof. All forward-looking statements are qualified in their entirety by this cautionary statement. This caution is made under the safe harbor provisions of Section 21E of the Private Securities Litigation Reform Act of 1995.

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DosePro^® and Relday^® are registered trademarks of Zogenix, Inc.

All other trademarks are of the associated companies.

Zogenix, Inc.

Condensed Consolidated Statements of Operations

(in thousands, except per share amounts)

(unaudited)

Zogenix, Inc.

Condensed Consolidated Balance Sheets

(in thousands)

(unaudited)