Exhibit 99.1

PRESS RELEASE

Juniper Pharmaceuticals Reports Third Quarter 2016 Financial Results

— Conference call at 8:30 a.m. EST today —

BOSTON, MA – November 15, 2016 – Juniper Pharmaceuticals, Inc. (Nasdaq: JNP) (“Juniper” or the “Company”), a women’s health therapeutics company, today announced financial results for the three- and nine- month periods ended September 30, 2016. Recent highlights include:

“Ongoing strong quarterly revenue growth provides continued cash flow which, coupled with the $11 million from Allergan, enables targeted investments in product development while also supporting our solid cash position,” said Alicia Secor, Juniper’s President and CEO.

“We continue to advance our IVR pipeline, targeting unmet and underserved needs in women’s health including overactive bladder, HRT and preterm birth,” Ms. Secor continued. “We are selectively evaluating acquisition and in-licensing opportunities with the goal of bringing in one or more women’s health therapeutics to enhance our product portfolio and establish a new trajectory to support our mission of building a leading women’s health company.”

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Juniper’s current 505(b)(2) product candidates are: JNP-0101, an oxybutynin IVR for the treatment of overactive bladder in women; JNP-0201, a combination estrogen + progesterone IVR for menopausal symptoms; and, JNP-0301, a progesterone IVR for the prevention of preterm birth in women with a short cervical length at mid-pregnancy.

Third Quarter Financial Results

Third quarter total revenues increased 5% to $11.6 million, compared with $11.0 million for the quarter ended September 30, 2015.

Product revenues were $7.1 million, an increase of $0.3 million, or 5%, versus the third quarter of last year, driven by continued in-market growth and new market sales of Crinone^® by Merck KGaA.

Service revenues were $3.3 million, a $0.1 million, or 4%, increase versus the third quarter of last year. While we experienced continued strong revenue growth in the local UK currency, the weak pound versus the U.S. dollar continues to dampen translated revenue. On a local currency basis, third quarter service revenues increased 22% year-over-year.

Royalty revenues, based on Allergan’s sales of Crinone^® in the U.S., increased by $0.1 million to $1.2 million.

Gross profit increased to $5.9 million as compared with $4.4 million in the prior year quarter.

Total operating expenses were $5.7 million in the third quarter of 2016. The $1.5 million increase as compared to the prior year quarter was driven by a $0.7 million increase in R&D spending and a $0.9 million increase in general and administrative costs.

Third quarter R&D expense was driven by costs associated with the now-concluded Phase 2 clinical trial of COL-1077. The increase in general and administrative costs was primarily driven by costs associated with organizational growth.

Juniper recorded net income of $0.2 million, or $0.02 per diluted share, in the third quarter of 2016, compared to net income of $0.4 million, or $0.03 per diluted share, in the same period of 2015.

Nine Months Financial Results

For the nine months ended September 30, 2016, total revenues increased 13% to $33.6 million, compared with $29.7 million for the nine months ended September 30, 2015.

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Product revenues were $20.7 million, an increase of $2.3 million, or 13%, versus the same period last year. Service revenues were $10.0 million, up $1.6 million, or 19%, versus the same period last year. On a local currency basis, service revenues in the first nine months of 2016 increased 31% year-over-year. Royalty revenues increased by $0.1 million to $3.0 million.

Gross profit increased to $15.1 million as compared with $12.7 million in the same period last year.

Total operating expenses were $19.0 million in the nine months ended September 30, 2016. The $5.5 million increase as compared to the prior year period was driven by a $3.1 million increase in R&D spending and a $2.5 million increase in general and administrative costs.

Juniper recorded a net loss of $3.7 million, or ($0.34) per diluted share, in the nine months ended September 30, 2016, compared to a net loss of $0.5 million, or ($0.05) per diluted share, in the same period of 2015.

Liquidity

Cash and cash equivalents increased to $15.0 million as of September 30, 2016, versus $13.0 million at June 30, 2016 and $13.9 million at December 31, 2015.

On November 15, 2016, the Company announced the monetization of U.S. Crinone^® royalty stream with Allergan, Inc. Juniper will record the $11 million payment and royalties for the month of October as royalty income in the fourth quarter of 2016.

Restatement

Financial results for prior periods discussed above are based on the Company’s restated financial results as filed on Forms 10-K/A and 10-Q/A filed on November 14, 2016 with the SEC.

Under the revised methodology, product revenue is recognized upon shipment to Merck KGaA at the minimum price (our direct manufacturing cost plus 20%). Amounts invoiced above the minimum price for countries where we are entitled to a percentage of Merck KGaA’s net revenue are recorded as deferred revenue. Upon receiving sell-through information from Merck KGaA, revenue is recorded to reflect the percentage of Merck KGaA’s net selling price for specific countries.

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Conference Call

As previously announced, Juniper’s management team will hold a conference call to discuss financial results for the third quarter ended September 30, 2016, as follows:

A replay of the teleconference will be available at approximately one hour after completion through Monday, November 21, 2016, at (877) 344-7529 (U.S.), (855) 669-9658 (Canada) or (412) 317-0088 (International). The conference ID for the replay is 10095855.

The archived webcast will be available for one year via the aforementioned URLs.

About Juniper Pharmaceuticals

Juniper Pharmaceuticals, Inc. is focused on developing therapeutics that address unmet medical needs in women’s health. The Company is advancing a pipeline of proprietary product candidates that leverage its differentiated intravaginal ring technology and the 505(b)(2) regulatory pathway. Juniper’s core operating business includes the Crinone^® (progesterone gel) franchise and Juniper Pharma Services, which provides high-end fee-for-service pharmaceutical development and clinical trials manufacturing to clients. Please visit www.juniperpharma.com for more information.

Juniper Pharmaceuticals™ is a trademark of Juniper Pharmaceuticals, Inc., in the U.S. and EU.

Crinone^® is a registered trademark of Merck KGaA, Darmstadt, Germany, outside the U.S. and of Allergan, Inc. in the U.S.

OneCrinone^® is a registered trademark of Merck KGaA, Darmstadt, Germany.

Forward Looking Statements

This press release contains “forward-looking statements” within the meaning of the Private Securities Litigation Reform Act of 1995, including statements relating to anticipated future financial performance; the timing of clinical trials for Juniper’s product candidates and the

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announcement of results from these trials; and the potential of Juniper’s IVR to improve the delivery of therapeutics to women. Management believes that these forward-looking statements are reasonable as and when made. However, such forward-looking statements involve known and unknown risks, uncertainties, and other factors that may cause actual results to differ materially from those projected in the forward-looking statements. These risks and uncertainties include, but are not limited to: risks associated with the drug development process generally, including the outcomes of planned clinical trials and the regulatory review process; the risk that the results of previously conducted studies involving our product candidates will not be repeated or observed in ongoing or future studies or following commercial launch, if such product candidates are approved; risks associated with obtaining, maintaining and protecting intellectual property; risks associated with Juniper Pharmaceuticals’ ability to enforce its patents against infringers and defend its patent portfolio against challenges from third parties; the risk of competition from currently approved therapies and from other companies developing products for similar uses; risk associated with Juniper Pharmaceuticals’ ability to manage operating expenses and/or obtain additional funding to support its business activities; and risks associated with Juniper Pharmaceuticals’ dependence on third parties. For a discussion of certain risks and uncertainties associated with Juniper Pharmaceuticals’ forward-looking statements, please review the Company’s reports filed with the SEC, including, but not limited to, its Annual Report on Form 10-K/A for the period ended December 31, 2015 and Quarterly Report on Form 10-Q for the period ended September 30, 2016 as filed with the SEC on November 14, 2016. Readers are cautioned not to place undue reliance on these forward-looking statements, which speak only as of the date on which they are made. These statements are based on management’s current expectations and Juniper Pharmaceuticals does not undertake any responsibility to revise or update any forward-looking statements contained herein, except as expressly required by law.

Contact

Amy Raskopf

Director, Corporate Communications, Juniper Pharmaceuticals, Inc.

(917) 673-5775 / ir@juniperpharma.com

Media:

Amy Covino

Tell Med Strategies

(201) 774-3111 / amy.covino@tmstrat.com

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Juniper Pharmaceuticals, Inc.

Condensed Consolidated Statements of Operations

(unaudited)

(in thousands, except per share data)

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Juniper Pharmaceuticals, Inc.

Condensed Consolidated Balance Sheets

(unaudited)

(in thousands)

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Source: Juniper Pharmaceuticals, Inc.

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