Stacey.Jurchison@PharmAthene.com

Phone: (410) 269-2610

PHARMATHENE REPORTS THIRD QUARTER 2012

ANNAPOLIS, MD - November 6, 2012

- PharmAthene, Inc. (NYSE Amex: PIP), a biodefense company developing medical countermeasures against biological and

chemical threats, today reported its financial results for the third quarter ended September 30, 2012.

President and Chief Executive Officer,

Eric I. Richman, said, "We made steady progress in the third quarter toward meeting our objectives. Most importantly, we

have worked expeditiously to address the U.S. Food and Drug Administration's (FDA) request for additional information on

our SparVax program, and are pleased to report that we expect to submit a complete response to the FDA shortly."

continued, "Regarding the ongoing litigation with SIGA, we are now entering the final stages of the appeals process, as all

legal briefs required from both PharmAthene and SIGA have been submitted to the Court and a date for oral argument has been set

for January 10, 2013. We remain confident in the merits of our case and the decision of the Delaware Court of Chancery and

look forward to a final ruling from the Delaware Supreme Court no later than the second quarter of 2013."

Linda L. Chang, Senior Vice President and

Chief Financial Officer, remarked, "We continue to meet our financial goals for 2012. At the end of the third quarter of

2012 we had cash and receivables totaling approximately $20.0 million compared to $18.7 million at December 31, 2011. Net cash

used in operations year-to-date is approximately $178,000. At this point, we are optimistic that we will be able to meet or exceed

our annual cash burn goal for 2012 of $6.0 million with cash burn defined as the change in our cash and cash equivalents."

Third Quarter 2012 Financial Results

For the third quarter ended September 30,

2012, PharmAthene recognized revenue of $6.7 million, compared to $5.3 million for the same period in 2011. Revenue in the third

quarter of 2012 was primarily from development contracts with the U.S. government for the Company's SparVax and rBChE

bioscavenger programs.

Research and development expenses for the

third quarter ended September 30, 2012 were $5.1 million, compared to $4.9 million for the same period in 2011. Research and development

expenses increased during the third quarter primarily as a result of higher direct expenses under the Company's SparVax

anthrax vaccine program although there were decreased costs for the Company's Valortim program and a reduction

in non-government funded internal research and development activities and other expenses.

Expenses associated with general and administrative

functions were $3.3 million for each of the three month periods ended September 30, 2012 and 2011.

For the third quarter of 2012, PharmAthene's

net loss attributable to common shareholders was $0.2 million, or $0.00 per share, compared to $0.03 million, or $0.00 per share,

in the same period of 2011. Included in the net loss for the nine months ended September 30, 2012 was a $1.2 million gain associated

with the realization of a cumulative translation adjustment and a $0.5 million gain reflecting the change in fair value of the

Company's derivative investments.

Cash Position and Accounts Receivables

As of September 30, 2012, the Company had

cash and cash equivalents and U.S. government billed and unbilled accounts receivables totaling approximately $20.0 million, compared

to $18.7 million at December 31, 2011. The increase in cash from December 31, 2011 to September 30, 2012 was primarily a result

of amounts provided under the term loan and revolving line of credit with GE Capital, partially offset by cash used in operations.

Conference Call and Webcast Information

PharmAthene management will be hosting

a conference call to discuss the Company's third quarter 2012 financial and operational results. The call is scheduled to

begin at 4:30 pm Eastern Time on Tuesday, November 6, 2012 and is expected to last approximately 30 minutes. The dial-in number

within the United States is 866-713-8564. The dial-in number for international callers is 617-597-5312. The participant passcode

A replay of the conference call will be

available beginning at approximately 6:30 pm Eastern Time on November 6, 2012 until approximately 11:59 p.m. Eastern Time on December

6, 2012. The dial-in number to access the replay from within the United States is 888-286-8010. For international callers, the

dial-in number is 617-801-6888. The participant passcode is 75262898.

The conference call will also be webcast

and can be accessed from the Company's website at www.PharmAthene.com. A link to the webcast may be found under the Investor

Relations section of the website.

About PharmAthene, Inc.

PharmAthene was formed to meet the critical needs of the United

States and its allies by developing and commercializing medical countermeasures against biological and chemical threats. PharmAthene's

lead product development programs include:

In addition, pursuant to a final judgment

issued May 31, 2012 from the Delaware Court of Chancery, PharmAthene is entitled to 50% of all net profits related to the sale

of SIGA Technologies' ST-246 and related products for 10 years following initial commercial sale of the drug

once SIGA earns the first $40 million in net profits from the sale of ST-246 and related products. ST-246

is a novel smallpox antiviral agent being developed by SIGA for the treatment and prevention of morbidity and mortality associated

with exposure to the causative agent of smallpox. For more information about PharmAthene, please visit www.PharmAthene.com.

Statement on Cautionary Factors

historical information presented herein, matters discussed may constitute forward-looking statements within the meaning of the

Private Securities Litigation Reform Act of 1995 that are subject to certain risks and uncertainties that could cause actual results

to differ materially from any future results, performance or achievements expressed or implied by such statements. Statements that

are not historical facts, including statements preceded by, followed by, or that include the words "potential"; "believe";

"anticipate"; "intend"; "plan"; "expect"; "estimate"; "could"; "may";

"should"; "will"; "project"; "potential"; or similar statements are forward-looking statements.

PharmAthene disclaims any intent or obligation to update these forward-looking statements other than as required by law. Risks

and uncertainties include risk associated with our interest in ST-246 , the reliability of the results of the studies

relating to human safety and possible adverse effects resulting from the administration of the Company's product candidates, unexpected

funding delays and/or reductions or elimination of U.S. government funding for one or more of the Company's development programs,

the award of government contracts to our competitors, unforeseen safety issues, challenges related to the development, scale-up,

technology transfer, and/or process validation of manufacturing processes for our product candidates, unexpected determinations

that these product candidates prove not to be effective and/or capable of being marketed as products, as well as risks detailed

from time to time in PharmAthene's Forms 10-K and 10-Q under the caption "Risk Factors" and in its other reports filed

with the U.S. Securities and Exchange Commission (the "SEC"). In particular, there is significant uncertainty

regarding the level and timing of sales of ST-246 and when and whether it will be approved by the U.S. FDA and

corresponding health agencies around the world. We cannot predict with certainty when SIGA will commence delivering any product

or will begin recognizing profit on the sale thereof and there can be no assurance that any profits received by SIGA and paid to

us will be significant. Furthermore, SIGA has filed an appeal with the Delaware Supreme Court challenging aspects of the Court

of Chancery decision, and there can be no assurances that the decision will not be reversed or that the remedy will not otherwise

be modified. In addition, we cannot predict how long the appeal will delay the receipt of payments, if any, from SIGA. Further,

significant additional non-clinical animal studies, human clinical trials, and manufacturing development work remain to be completed

for all of our product candidates, and with FDA's August 2012 clinical hold of SparVax , it is unclear

when, if ever, we can re-initiate human clinical trials for that product candidate.

Copies of PharmAthene's public disclosure

filings are available from its investor relations department and our website under the investor relations tab at www.PharmAthene.com.

CONDENSED CONSOLIDATED BALANCE SHEETS

UNAUDITED CONDENSED CONSOLIDATED STATEMENTS