UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

WASHINGTON, DC 20549





FORM 10-K/A

(Amendment No. 1)







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

For the fiscal year ended December 31, 2015



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

For the Transition Period from
 to

Commission File Number: 001-35405





CEMPRA, INC.

(Exact name of registrant specified in its charter)







|                                                               |  |                                                          |  |                                     
|-------------------------------------------------------------- |  | -------------------------------------------------------- |  | ------------------------------------
|Delaware                                                       |  | 2834                                                     |  | 45-4440364                          
|(State or Other Jurisdiction of
Incorporation or Organization) |  | (Primary Standard Industrial
Classification Code Number) |  | (I.R.S. Employer
Identification No.)

6320 Quadrangle Drive, Suite 360

Chapel Hill, NC 27517

(Address of Principal Executive Offices)

(919) 313-6601

(Telephone Number, Including Area Code)

Securities Registered Pursuant to Section 12(b) of the Exchange Act:



|                               |  |                                     
|------------------------------ |  | ------------------------------------
|Title of Each Class            |  | Name of Exchange on which
Registered
|Common Stock, $0.001 Par Value |  | Nasdaq Global Market                

Securities Registered Pursuant to Section 12(g) of the Act: None





Indicate by check mark if the registrant is a well-known seasoned issuer, as defined in Rule 405 of the Securities Act.    Yes   ̈    No  x

Indicate by check mark
if the registrant is not required to file reports pursuant to Section 13 or Section 15(d) of the Exchange Act.    Yes   ̈    No  x

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 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
if disclosure of delinquent filers pursuant to Item 405 of Regulation S-K is not contained herein, and will not be contained, to the best of the registrants knowledge, in definitive proxy or information statements incorporated by
reference in Part III of this Form 10-K or any amendment to this Form 10-K.   ̈

Indicate by
check mark whether the registrant is a large accelerated filer, an accelerated filer, or a smaller reporting company. See definitions of large accelerated filer, accelerated filer and smaller reporting company in
Rule 12b-2 of the Exchange Act. (Check one):



|                        |  |                                                  |  |                           |  |  
|----------------------- |  | ------------------------------------------------ |  | ------------------------- |  | -
|Large accelerated filer |  | x                                                |  | Accelerated filer         |  |  ̈
|                        |  |                                                  | 
|Non-accelerated filer   |  |  ̈  (Do not check if a smaller reporting company) |  | Smaller reporting company |  |  ̈

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

The aggregate market value of the voting stock held by non-affiliates of the registrant, as of June 30, 2015, was approximately $1.2 billion. Such
aggregate market value was computed by reference to the closing price of the common stock as reported on the Nasdaq Global Market on June 30, 2015. For purposes of making this calculation only, the registrant has defined affiliates as
including only directors and executive officers and shareholders holding greater than 10% of the voting stock of the registrant as of June 30, 2015.

As of February 18, 2016 there were 48,169,733 shares of the registrants common stock, $0.001 par value, outstanding.





DOCUMENTS INCORPORATED BY REFERENCE

Certain portions of the registrants definitive Proxy Statement for its 2016 Annual Meeting of Stockholders are incorporated herein by reference, as
indicated in Part III.









---

EXPLANATORY NOTE

Cempra, Inc. is filing this Amendment No. 1 (the Amendment) to our Annual Report on Form 10-K for the fiscal year ended
December 31, 2015, as originally filed with the Securities and Exchange Commission (SEC) on February 25, 2016 (the Original Form 10-K), to (i) amend Item 5(a) of Part II to provide the high and low sales
prices for our common stock for each quarter of 2014 and 2015 and (ii) amend Item 15(b) of Part IV to re-file two agreements that were filed as exhibits to the Original Form 10-K to reflect the inclusion of information that we had
previously requested be treated confidentially. In addition, Item 15(b) of Part IV is being amended solely to file as exhibits certain new certifications in accordance with Rule 13a-14(a) promulgated by the SEC under the Securities Exchange Act
of 1934.

Except as described above, no other changes have been made to the Original Form 10-K. This Amendment No. 1 continues to
speak as of the date of the Original Form 10-K and we have not updated the disclosure herein to reflect any events that occurred at a later date other than as expressly stated herein. Accordingly, this Amendment No. 1 should be read in
conjunction with the Original Form 10-K and with our filings made with the SEC subsequent to the filing of the Original Form 10-K.



---

PART II



|Item 5. | Market for Registrants Common Equity, Related Stockholder Matters and Issuer Purchases of Equity Securities
|------- | ------------------------------------------------------------------------------------------------------------

Our common stock is traded under the symbol CEMP and is quoted on the NASDAQ Global Market. The following table sets forth the high
and low sale prices of our common stock, as reported on the NASDAQ Global Market in each quarter of 2015 and 2014.



|               |  |      |       |  |     |   |       | 
|-------------- |  | ---- | ----- |  | --- | - | ----- | 
|               |  | High |       |  | Low |  
|2015           |  |      |       |  |     |   |       | 
|Fourth quarter |  | $    | 34.79 |  |     | $ | 15.43 | 
|Third quarter  |  | $    | 46.99 |  |     | $ | 24.00 | 
|Second quarter |  | $    | 39.68 |  |     | $ | 31.15 | 
|First quarter  |  | $    | 41.63 |  |     | $ | 21.52 | 
|               |  |     
|2014           |  |      |       |  |     |   |       | 
|Fourth quarter |  | $    | 24.71 |  |     | $ | 10.86 | 
|Third quarter  |  | $    | 11.60 |  |     | $ | 8.55  | 
|Second quarter |  | $    | 12.00 |  |     | $ | 8.10  | 
|First quarter  |  | $    | 15.39 |  |     | $ | 10.60 | 



---

PART IV



|Item 15. | Exhibits, Financial Statement Schedules
|-------- | ---------------------------------------

(3) Exhibits. The following exhibits are included herein or
incorporated herein by reference:



|            |  |                                                                                                                                                                  |  |                   |  |            |  |                |  |               
|----------- |  | ---------------------------------------------------------------------------------------------------------------------------------------------------------------- |  | ----------------- |  | ---------- |  | -------------- |  | --------------
|Exhibit
No. |  | Description                                                                                                                                                      |  | Registrants
Form |  | Dated      |  | Exhibit
Number |  | Filed
Herewith
|            |  |                                                                                                                                                                  |  |                   | 
|2.1         |  | Form of Plan of Conversion of Cempra Holdings, LLC.                                                                                                              |  | S-1               |  | 10/12/2011 |  | 2.1            |  |               
|            |  |                                                                                                                                                                  |  |                   | 
|3.1         |  | Certificate of Incorporation of Cempra, Inc.                                                                                                                     |  | S-1/A             |  | 1/13/2012  |  | 3.1            |  |               
|            |  |                                                                                                                                                                  |  |                   | 
|3.2         |  | Form of Bylaws of Cempra, Inc.                                                                                                                                   |  | S-1               |  | 10/12/2011 |  | 3.2            |  |               
|            |  |                                                                                                                                                                  |  |                   | 
|4.1         |  | Specimen of Common Stock Certificate of Cempra, Inc.                                                                                                             |  | S-1/A             |  | 11/22/2011 |  | 4.1            |  |               
|            |  |                                                                                                                                                                  |  |                   | 
|4.2         |  | Form of Registration Rights Agreement by and among Cempra, Inc. and certain of its stockholders, to be effective upon the corporate conversion.                  |  | S-1               |  | 10/12/2011 |  | 4.2            |  |               
|            |  |                                                                                                                                                                  |  |                   | 
|10.1        |  | Forms of Indemnification Agreements by and between Cempra, Inc. and its directors.                                                                               |  | S-1               |  | 10/12/2011 |  | 10.1           |  |               
|            |  |                                                                                                                                                                  |  |                   | 
|10.2        |  | Cempra, Inc. Sixth Amended and Restated 2006 Stock Plan.                                                                                                         |  | S-1/A             |  | 1/13/2012  |  | 10.2           |  |               
|            |  |                                                                                                                                                                  |  |                   | 
|10.3        |  | Cempra, Inc. 2011 Equity Incentive Plan and Form of Stock Option Agreement thereunder.                                                                           |  | S-1/A             |  | 1/13/2012  |  | 10.3           |  |               
|            |  |                                                                                                                                                                  |  |                   | 
|10.4*       |  | Collaborative Research and Development and License Agreement dated March 31, 2006, by and between Cempra Pharmaceuticals, Inc. and Optimer Pharmaceuticals, Inc. |  | S-1               |  | 10/12/2011 |  | 10.4           |  |               
|            |  |                                                                                                                                                                  |  |                   | 
|10.5*       |  | Supply Agreement effective March 15, 2011, by and among CEM-102 Pharmaceuticals, Inc., Ercros S.A. and Gyma Laboratories of America, Inc.                        |  | S-1               |  | 10/12/2011 |  | 10.5           |  |               
|            |  |                                                                                                                                                                  |  |                   | 
|10.6        |  | Office Lease Agreement dated November 9, 2011 between Cempra Pharmaceuticals, Inc. and Property Reserve, Inc.                                                    |  | S-1/A             |  | 11/22/2011 |  | 10.6           |  |               
|            |  |                                                                                                                                                                  |  |                   | 
|10.7        |  | Loan and Security Agreement dated December 20, 2011 between Cempra Holdings, LLC and Hercules Technology Growth Capital, Inc.                                    |  | S-1/A             |  | 12/22/2011 |  | 10.7           |  |               
|            |  |                                                                                                                                                                  |  |                   | 
|10.8        |  | Secured Promissory Note dated December 20, 2011, issued by Cempra Holdings, LLC to Hercules Technology Growth Capital, Inc.                                      |  | S-1/A             |  | 12/22/2011 |  | 10.8           |  |               
|            |  |                                                                                                                                                                  |  |                   | 
|10.9*       |  | License Agreement, effective June 12, 2012, between The Scripps Research Institute and Cempra Pharmaceuticals, Inc.                                              |  | 10-Q              |  | 8/08/2012  |  | 10.9           |  |               
|            |  |                                                                                                                                                                  |  |                   | 
|10.10       |  | 2011 Equity Incentive Plan, as amended May 23, 2013.                                                                                                             |  | 10-Q              |  | 7/31/2013  |  | 10.3           |  |               
|            |  |                                                                                                                                                                  |  |                   | 
|10.11*      |  | Exclusive License and Development Agreement by and between Cempra Pharmaceuticals, Inc. and Toyama Chemical Co., Ltd., dated May 8, 2013.                        |  | 10-Q              |  | 7/31/2013  |  | 10.13          |  |               
|            |  |                                                                                                                                                                  |  |                   | 
|10.12*      |  | Supply Agreement by and between Cempra Pharmaceuticals, Inc. and Toyama Chemical Co., Ltd., dated May 8, 2013.                                                   |  | 10-Q              |  | 7/31/2013  |  | 10.14          |  |               
|            |  |                                                                                                                                                                  |  |                   | 
|10.13*      |  | Contract by and between Cempra, Inc. and the Biomedical Advanced Research and Development Authority, dated May 24, 2013.                                         |  | 10-Q              |  | 7/31/2013  |  | 10.15          |  |               
|            |  |                                                                                                                                                                  |  |                   | 
|10.14*      |  | Development and Supply Agreement by and between Cempra Pharmaceuticals, Inc. and Hospira Worldwide, Inc. effective as of July 1, 2013.                           |  | 10-Q/A            |  | 11/08/2013 |  | 10.18          |  |               



---

|      |  |                                                                                                                                                                                                                                                                                                    |  |      |  |            |  |       |  | 
|----- |  | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |  | ---- |  | ---------- |  | ----- |  | 
|10.15 |  | Amendment No. 1, effective as of September 26, 2013 to Exclusive License And Development Agreement by and between Cempra Pharmaceuticals, Inc. and Toyama Chemical Co., Ltd, dated May 8, 2013.                                                                                                    |  | 10-Q |  | 10/29/2013 |  | 10.19 |  | 
|      |  |                                                                                                                                                                                                                                                                                                    |  |      | 
|10.16 |  | Amendment No. 2 to Loan and Security Agreement, dated May 31, 2013, by and among Cempra, Inc., and each of its subsidiaries signatory thereto, and Hercules Capital Funding Trust 2012-1, as a lender and Hercules Technology Growth
Capital, Inc., as a lender and as an agent for the lenders.   |  | 8-K  |  | 6/06/2013  |  | 10.12 |  | 
|      |  |                                                                                                                                                                                                                                                                                                    |  |      | 
|10.17 |  | Form of Employment Agreement by and between Cempra, Inc. and Prabhavathi B. Fernandes, Ph.D.                                                                                                                                                                                                       |  | 8-K  |  | 8/13/2013  |  | 10.16 |  | 
|      |  |                                                                                                                                                                                                                                                                                                    |  |      | 
|10.18 |  | Form of Change in Control Severance Agreement by and between Cempra, Inc. and Prabhavathi B. Fernandes, Ph.D.                                                                                                                                                                                      |  | 8-K  |  | 8/13/2013  |  | 10.17 |  | 
|      |  |                                                                                                                                                                                                                                                                                                    |  |      | 
|10.19 |  | First Amendment, dated May 17, 2013, to Office Lease Agreement dated November 9, 2011 between Cempra Pharmaceuticals, Inc., and Property Reserve, Inc.                                                                                                                                             |  | 10-K |  | 2/28/2014  |  | 10.21 |  | 
|      |  |                                                                                                                                                                                                                                                                                                    |  |      | 
|10.20 |  | Second Amendment, dated August 13, 2013, to Office Lease Agreement dated November 9, 2011 between Cempra Pharmaceuticals, Inc., and Property Reserve, Inc.                                                                                                                                         |  | 10-K |  | 2/28/2014  |  | 10.22 |  | 
|      |  |                                                                                                                                                                                                                                                                                                    |  |      | 
|10.21 |  | Amendment No. 3 to Loan and Security Agreement, dated March 27, 2014, by and among Cempra, Inc., and each of its subsidiaries signatory thereto, and Hercules Capital Funding Trust 2012-1, as a lender and Hercules Technology Growth
Capital, Inc., as a lender and as an agent for the lenders. |  | 8-K  |  | 10/17/2014 |  | 10.23 |  | 
|      |  |                                                                                                                                                                                                                                                                                                    |  |      | 
|10.22 |  | Third Amendment, dated March 31, 2014, to Office Lease Agreement dated November 9, 2011 between Cempra, Inc. and Property Reserve, Inc.                                                                                                                                                            |  | 10-Q |  | 4/29/2014  |  | 10.24 |  | 
|      |  |                                                                                                                                                                                                                                                                                                    |  |      | 
|10.23 |  | Change in Control Severance Agreement, dated May 23, 2014, by and between Cempra, Inc. and Mark W. Hahn.                                                                                                                                                                                           |  | 8-K  |  | 5/29/2014  |  | 10.25 |  | 
|      |  |                                                                                                                                                                                                                                                                                                    |  |      | 
|10.24 |  | Amendment No. 4 to Loan and Security Agreement, dated June 30, 2014, by and among Cempra, Inc., and each of its subsidiaries signatory thereto, and Hercules Capital Funding Trust 2012-1, as a lender and Hercules Technology Growth
Capital, Inc., as a lender and as an agent for the lenders.  |  | 10-Q |  | 7/29/2014  |  | 10.25 |  | 
|      |  |                                                                                                                                                                                                                                                                                                    |  |      | 
|10.25 |  | Amendment, dated November 13, 2014, to Contract by and between Cempra Pharmaceuticals, Inc. and the Biomedical Advanced Research and Development Agency, dated May 24, 2013.                                                                                                                       |  | 10-K |  | 2/29/2015  |  | 10.27 |  | 
|      |  |                                                                                                                                                                                                                                                                                                    |  |      | 
|10.26 |  | Change in Control Severance Agreement, dated May 23, 2014, by and between Cempra, Inc. and David Moore                                                                                                                                                                                             |  | 10-Q |  | 4/30/2015  |  | 10.1  |  | 
|      |  |                                                                                                                                                                                                                                                                                                    |  |      | 
|10.27 |  | Loan and Security Agreement, dated as of July 10, 2015, by and among Comerica Bank and Cempra, Inc., Cempra Pharmaceuticals, Inc. and CEM-102 Pharmaceuticals, Inc.                                                                                                                                |  | 8-K  |  | 7/16/2015  |  | 10.1  |  | 
|      |  |                                                                                                                                                                                                                                                                                                    |  |      | 
|10.28 |  | Form of Change in Control Severance Agreement by and between Cempra, Inc. and David W. Oldach, M.D.                                                                                                                                                                                                |  | 8-K  |  | 10/19/2015 |  | 10.1  |  | 
|      |  |                                                                                                                                                                                                                                                                                                    |  |      | 
|10.29 |  | Amendment to Form of Employment Agreement by and between Cempra, Inc. and Prabhavathi B. Fernandes, Ph.D.                                                                                                                                                                                          |  | 8-K  |  | 10/19/2015 |  | 10.2  |  | 



---

|        |  |                                                                                                                                                        |  |      |  |            |  |      |  |  
|------- |  | ------------------------------------------------------------------------------------------------------------------------------------------------------ |  | ---- |  | ---------- |  | ---- |  | -
|10.30   |  | Amendment to Form of Change in Control Severance Agreement by and between Cempra, Inc. and Prabhavathi Fernandes, Ph.D.                                |  | 8-K  |  | 10/19/2015 |  | 10.3 |  |  
|        |  |                                                                                                                                                        |  |      | 
|10.31   |  | Amendment to Form of Change in Control Severance Agreement by and between Cempra, Inc. and Mark W. Hahn                                                |  | 8-K  |  | 10/19/2015 |  | 10.4 |  |  
|        |  |                                                                                                                                                        |  |      | 
|10.32   |  | Amendment to Form of Change in Control Severance Agreement by and between Cempra, Inc. and David Moore                                                 |  | 8-K  |  | 10/19/2015 |  | 10.5 |  |  
|        |  |                                                                                                                                                        |  |      | 
|10.34** |  | Option and License Agreement, dated January 29, 2016, between Cempra Pharmaceuticals, Inc. and Macrolide Pharmaceuticals, Inc.                         |  |      |  |            |  |      |  | X
|        |  |                                                                                                                                                        |  |      | 
|10.35** |  | API Manufacturing and Supply Agreement, entered into January 18, 2016, by and between Cempra, Inc. and FUJIFILM Finechemicals Co., Ltd.                |  |      |  |            |  |      |  | X
|        |  |                                                                                                                                                        |  |      | 
|21.1    |  | List of subsidiaries of Cempra Holdings, LLC.                                                                                                          |  | S-1  |  | 10/12/2011 |  | 21.1 |  |  
|        |  |                                                                                                                                                        |  |      | 
|23.1    |  | Consent of Independent Registered Public Accounting Firm                                                                                               |  | 10-K |  | 2/25/2016  |  | 23.1 |  |  
|        |  |                                                                                                                                                        |  |      | 
|31.1    |  | Certification of the Chief Executive Officer Pursuant to Section 302 of the Sarbanes-Oxley Act of 2002.                                                |  |      |  |            |  |      |  | X
|        |  |                                                                                                                                                        |  |      | 
|31.2    |  | Certification of the Chief Financial Officer Pursuant to Section 302 of the Sarbanes-Oxley Act of 2002.                                                |  |      |  |            |  |      |  | X
|        |  |                                                                                                                                                        |  |      | 
|32.1    |  | Certification of the Chief Executive Officer Pursuant to 18 U.S. C. Section 1350 as Adopted Pursuant to Section 906 of the Sarbanes-Oxley Act of 2002. |  | 10-K |  | 2/25/2016  |  | 32.1 |  |  
|        |  |                                                                                                                                                        |  |      | 
|32.2    |  | Certification of the Chief Financial Officer Pursuant to 18 U.S. C. Section 1350 as Adopted Pursuant to Section 906 of the Sarbanes-Oxley Act of 2002. |  | 10-K |  | 2/25/2016  |  | 32.2 |  |  
|        |  |                                                                                                                                                        |  |      | 
|101     |  | Financials in XBRL format.                                                                                                                             |  | 10-K |  | 2/25/2016  |  | 101  |  |  



|* | The Registrant has received confidential treatment with respect to portions of this exhibit. Those portions have been omitted and filed separately with the Securities and Exchange Commission pursuant to a confidential
treatment request.
|- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

|** | Confidential treatment has been requested with respect to certain portions of this exhibit. Omitted portions have been filed separately with the SEC.
|-- | -----------------------------------------------------------------------------------------------------------------------------------------------------



---

SIGNATURES

Pursuant to the requirements of the Section 13 or 15(d) of the Securities Exchange Act of 1934, the Registrant has duly caused this
Amendment No. 1 on Form 10-K/A to be signed on its behalf by the undersigned, thereunto duly authorized.



|              |  |  |  |              |  |                                                                   
|------------- |  |  |  | ------------ |  | ------------------------------------------------------------------
|              |  |  |  | CEMPRA, INC.
|              |  | 
|June 17, 2016 |  |  |  |             
|              |  |  | 
|              |  |  |  | By:          |  | /s/ Prabhavathi Fernandes, Ph.D.                                  
|              |  |  |  |              |  | Prabhavathi Fernandes, Ph.D. President and
Chief Executive Officer