UNITED STATES
SECURITIES AND EXCHANGE COMMISSION
Washington, D.C. 20549



FORM 10-Q/A

(Amendment No. 1)

(Mark One)

|x | QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934
|- | ---------------------------------------------------------------------------------------



For the quarterly period ended September
30, 2014

or



| ̈ | TRANSITION REPORT UNDER SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934
|- | ----------------------------------------------------------------------------------



Commission File Number: 001-32587



PHARMATHENE, INC.

(Exact name of registrant as specified in
its charter)



|Delaware                                                       |  | 20-2726770                          
|-------------------------------------------------------------- |  | ------------------------------------
|(State or other jurisdiction of incorporation or
organization) |  | (I.R.S. Employer Identification No.)
|                                                               |  |                                     
|One Park Place, Suite 450, Annapolis, Maryland                 |  | 21401                               
|(Address of principal executive offices)                       |  | (Zip Code)                          



(410) 269-2600
(Registrant’s telephone number, including area code)



Indicate by check mark whether the registrant
(1) has filed all reports required to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during the preceding
12 months (or for such shorter period that the registrant was required to file such reports), and (2) has been subject to such
filing requirements for the past 90 days. Yes x No  ̈



Indicate by check mark whether the registrant
has submitted electronically and posted on its corporate Web site, if any, every Interactive Data file required to be submitted
and posted pursuant to Rule 405 of Regulation S-T (§232.405 of this chapter) during the preceding 12 months (or for such shorter
period that the registrant was required to submit and post such files). Yes x No  ̈



Indicate by check mark whether the registrant
is a large accelerated filer, an accelerated filer, a non-accelerated filer, or a smaller reporting company. See the definitions
of “large accelerated filer,” “accelerated filer” and “smaller reporting company” in Rule 12b-2
of the Exchange Act.



|Large Accelerated Filer  ̈                     |  | Accelerated Filer  ̈        
|--------------------------------------------- |  | ---------------------------
|                                              |  |                            
|Non-Accelerated Filer x                       |  | Smaller Reporting Company  ̈
|(Do not check if a smaller reporting company) |  |                            



Indicate by check mark whether the registrant
is a shell company (as defined in Rule 12b-2 of the Act). Yes  ̈ No x



Indicate the number
of shares outstanding of each of the issuer’s classes of common stock, as of the latest practicable date: The number of shares
of the registrant’s Common Stock, par value $0.0001 per share, outstanding as of November 3, 2014 was 63,373,584.











EXPLANATORY NOTE



PharmAthene, Inc. (the “Company”)
is filing this Amendment No. 1 on Form 10-Q/A (“Amendment”) to amend its Quarterly Report on Form 10-Q for the quarter
ended September 30, 2014 (the “Form 10-Q”), which was originally filed with the Securities and Exchange Commission
on November 6, 2014. The purpose of this Amendment is to refile Exhibit 10.61, which was originally filed with the Form 10-Q, without
redaction in response to suggestions provided by the staff of the Securities and Exchange Commission relating to the confidential
treatment request previously filed by the Company with respect to Exhibit 10.61.



This Amendment speaks as of the original
filing date and does not reflect events occurring after the filing of the Form 10-Q or modify or update disclosures that may be
affected by subsequent events. No revisions are being made to the Company’s financial statements or any other disclosure
contained in the Form 10-Q.



This Amendment is an exhibit-only filing.
Except for the changes to Exhibit 10.61, this Amendment does not otherwise update any exhibits as originally filed or previously
amended.



In addition, as required by Rule 12b-15
under the Securities Exchange Act of 1934, as amended (the “Exchange Act”), new certifications by the Company’s
principal executive officer and principal financial officer are filed herewith as exhibits to this Amendment pursuant to Rule 13a-14(a)
of the Exchange Act. The Company is not including certifications pursuant to Section 1350 of Chapter 63 of Title 18 of the United
States Code (18 U.S.C. 1350) as no financial statements are being filed with this Amendment.











Item 6. Exhibits



|No.      |  | Description                                                                                                                                                                                                                                                   
|-------- |  | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
|         |  |                                                                                                                                                                                                                                                               
|10.61#   |  | Contract with the National Institute of Allergy and Infectious Diseases of the National Institutes of Health for the Development of Vaccine Formulations Effective Against NIAID Priority Pathogens, dated September 9, 2014 (Contract No. HHSN272201400040C).
|         |  |                                                                                                                                                                                                                                                               
|31.1#    |  | Certification of Principal Executive Officer Pursuant to SEC Rule 13a-14(a)/15d-14(a)                                                                                                                                                                         
|         |  |                                                                                                                                                                                                                                                               
|31.2#    |  | Certification of Principal Financial Officer Pursuant to SEC Rule 13a-14(a)/15d-14(a)                                                                                                                                                                         
|         |  |                                                                                                                                                                                                                                                               
|101.INS* |  | Instance Document                                                                                                                                                                                                                                             
|         |  |                                                                                                                                                                                                                                                               
|101.SCH* |  | XBRL Taxonomy Extension Schema Document                                                                                                                                                                                                                       
|         |  |                                                                                                                                                                                                                                                               
|101.CAL* |  | XBRL Taxonomy Extension Calculation Linkbase Document                                                                                                                                                                                                         
|         |  |                                                                                                                                                                                                                                                               
|101.DEF* |  | XBRL Taxonomy Extension Definition Linkbase Document                                                                                                                                                                                                          
|         |  |                                                                                                                                                                                                                                                               
|101.LAB* |  | XBRL Taxonomy Extension Label Linkbase Document                                                                                                                                                                                                               
|         |  |                                                                                                                                                                                                                                                               
|101.PRE* |  | XBRL Taxonomy Extension Presentation Linkbase Document                                                                                                                                                                                                        








# Filed herewith.



* Previously furnished with our
Quarterly Report on Form 10-Q for the quarterly period ended September 30, 2014, as filed on November 6, 2014.











SIGNATURES



Pursuant to the requirements of Section
13 or 15(d) of the Securities Exchange Act of 1934, the Registrant has duly caused the report to be signed on its behalf by the
undersigned, thereunto duly authorized.



|                         | PHARMATHENE, INC.                                                     
|------------------------ | ----------------------------------------------------------------------
|                         |                                                                       
|Dated: November 22, 2016 | By:                                                                   
|                         | Name: John M. Gill                                                    
|                         | Title: President and Chief Executive Officer                          
|                         |                                                                       
|Dated: November 22, 2016 | By:                                                                   
|                         | Name: Philip MacNeill                                                 
|                         | Title: Vice President, Chief Financial Officer,Treasurer and Secretary