UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

WASHINGTON, D.C. 20549





FORM 10-K/A Amendment No. 1




(Mark One)

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



For the fiscal year ended December 31, 2017



or



|☐ |  | 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 001-36289



PROTEON THERAPEUTICS, INC.

(Exact name of registrant as
specified in its charter)









|Delaware                                                               |  | 20-4580525                                  
|---------------------------------------------------------------------- |  | --------------------------------------------
|(State or other jurisdiction of
        incorporation or organization) |  | (I.R.S. Employer
        Identification No.)



|200 West Street
        Waltham, MA      |  | 02451     
|---------------------------------------- |  | ----------
|(Address of principal executive offices) |  | (Zip Code)



Registrant’s telephone number, including area code: (781) 890-0102



Securities registered pursuant to Section 12(b) of the
Act:



|Title of each class            |  | Name of each 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



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



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  ☐  No



Indicate by check mark whether the registrant has submitted electronically
and posted on its corporate website, 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    ☐  No










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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 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.   o





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



|Large accelerated filer  ☐                    |  | Accelerated filer  ☐        
|--------------------------------------------- |  | ----------------------------
|                                              |  |                             
|Non-accelerated filer  ☒                      |  | Smaller reporting company  ☐
|(Do not check if a smaller reporting company) |  | Emerging growth company  ☒  



If an emerging growth company, indicate by check mark if the registrant
has elected not to use the extended transition period for complying with any new or revised financial accounting standards provided
pursuant to Section 13(a) of the Exchange Act.    ☐



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



The aggregate market value of the voting and non-voting common equity
held by non-affiliates of the registrant, based on the closing price for such stock as reported on the NASDAQ Global Market on
June 30, 2017, the last business day of the registrant’s most recently completed second quarter, was: $16.3 million.



As of March 9, 2018 there were 17,674,729 shares of the registrant’s
common stock, par value $0.001 per share, outstanding.















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Explanatory Note



This Amendment No. 1 on Form 10-K/A amends Proteon Therapeutics, Inc.’s Annual
Report on Form 10-K (the “Amended Filing”) for the period ended December 31, 2017, which was originally filed with
the Securities and Exchange Commission (the “SEC”) on March 14, 2018 (the “Original 10-K”). This Amended
Filing is being filed to amend Item 6 (Selected Financial Data) of the Original 10-K solely to correct scrivener’s errors
in the presentation of interest expense in the selected consolidated statements of operations data for each of the years ended
December 31, 2014 and 2013 and the table of selected consolidated balance sheet data at December 31, 2015, 2014 and 2013 included
in such Item 6. No other items are being amended except as described in this Explanatory Note and this Amended Filing does not
reflect any events occurring after the date of the Original 10-K.



In accordance with applicable SEC rules, this Amended Filing includes new certifications
required by Rule 13a-14 under the Securities Exchange Act of 1934, as amended, from our Principal Executive Officer and Principal
Financial Officer dated as of the date of this Amended Filing.















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Item 6.  Selected Financial Data



The selected consolidated statements of operations
data for each of the three years ended December 31, 2017, 2016 and 2015, and the selected consolidated balance sheet data
at December 31, 2017 and 2016 have been derived from our audited consolidated financial statements included elsewhere in this
Annual Report on Form 10-K. The selected consolidated statement of operations data for the year ended December 31, 2014 and
2013 and the selected consolidated balance sheet data at December 31, 2015, 2014 and 2013 have been derived from our audited consolidated
financial statements for such years not included in this Annual Report on Form 10-K. Our historical results for any prior period
are not necessarily indicative of results to be expected in any future period, and our interim period results are not necessarily
indicative of results to be expected in any future period.



The information set forth below should be read
in conjunction with the “Management’s Discussion and Analysis of Financial Condition and Results of Operations”
section of this Annual Report on Form 10-K and with our consolidated financial statements and notes thereto included elsewhere
in this Annual Report on Form 10-K. The selected consolidated financial data in this section are not intended to replace the
consolidated financial statements and are qualified in their entirety by the consolidated financial statements and related notes
included elsewhere in this Annual Report on Form 10-K.





|                                                                                                                              |  | Proteon Therapeutics, Inc.                     
|----------------------------------------------------------------------------------------------------------------------------- |  | -----------------------------------------------
|                                                                                                                              |  | Year Ended December 31,                        
|                                                                                                                              |  | 2017                                           
|                                                                                                                              |  | (in thousands, except share and per share data)
|Revenue                                                                                                                       |  | $                                              
|Operating expenses:                                                                                                           |  |                                                
|Research and development                                                                                                      |  |                                                
|General and administrative                                                                                                    |  |                                                
|Total operating expenses                                                                                                      |  |                                                
|Loss from operations                                                                                                          |  |                                                
|Other income (expense):                                                                                                       |  |                                                
|Investment income                                                                                                             |  |                                                
|Interest expense                                                                                                              |  |                                                
|Other income (expense)                                                                                                        |  |                                                
|Total other income (expense)                                                                                                  |  |                                                
|Net loss                                                                                                                      |  | $                                              
|Foreign currency translation adjustment                                                                                       |  | $                                              
|Unrealized (loss) gain on available-for-sale investments                                                                      |  |                                                
|Comprehensive loss                                                                                                            |  | $                                              
|Reconciliation of net loss to net loss attributable to common stockholders:                                                   |  |                                                
|Net loss                                                                                                                      |  | $                                              
|Accretion of redeemable convertible preferred stock to redemption value                                                       |  |                                                
|Accretion of convertible preferred stock to redemption value                                                                  |  |                                                
|Net loss attributable to common stockholders                                                                                  |  | $                                              
|Net loss per share attributable to common stockholders - basic and diluted                                                    |  | $                                              
|Weighted-average common shares outstanding used in net loss per share attributable to common stockholders - basic and diluted |  |                                                



Supplemental disclosure of stock-based compensation expense:



Included in operating expenses, above, are the following amounts
for non-cash stock-based compensation expense:



|Research and development   |  | $ | 1,109 |  |  | $ | 1,114 |  |  | $ | 650   |  |  | $ | 114 |  |  | $ | 106 | 
|-------------------------- |  | - | ----- |  |  | - | ----- |  |  | - | ----- |  |  | - | --- |  |  | - | --- | 
|General and administrative |  |   | 2,118 |  |  |   | 2,229 |  |  |   | 1,514 |  |  |   | 345 |  |  |   | 49  | 
|Total                      |  | $ | 3,227 |  |  | $ | 3,343 |  |  | $ | 2,164 |  |  | $ | 459 |  |  | $ | 155 | 











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|                                                          |  | December 31,  
|--------------------------------------------------------- |  | --------------
|                                                          |  | 2017          
|                                                          |  | (in thousands)
|Balance Sheet Data:                                       |  |               
|Cash, cash equivalents and available-for-sale investments |  | $             
|Working capital                                           |  |               
|Total assets                                              |  |               
|Convertible preferred stock                               |  |               
|Preferred stock                                           |  |               
|Common stock and additional paid-in-capital               |  |               
|Total stockholders’ equity (deficit)                      |  |               















5









SIGNATURES



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



|PROTEON THERAPEUTICS, INC.                                                                                                                         |  |               
|-------------------------------------------------------------------------------------------------------------------------------------------------- |  | --------------
|                                                                                                                                                   |  |               
|By: /s/ George A. Eldridge                                                                                                                         |  | March 28, 2018
|George A. Eldridge
        Senior Vice President, Chief Financial Officer, Treasurer and
        Assistant Secretary (Principal Financial Officer) |  |               

























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EXHIBIT INDEX



|Exhibit No. |    | Description                                                                                                                                                                                          
|----------- | -- | -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
|31.1        | *  | Certification of Principal Executive Officer Required Under Rule 13a-14(a) and 15d-14(a) of the
    Securities Exchange Act of 1934, as amended.                                                     
|            |    |                                                                                                                                                                                                      
|31.2        | *  | Certification of Principal Financial Officer Required Under Rule 13a-14(a) and 15d-14(a) of the
    Securities Exchange Act of 1934, as amended.                                                     
|            |    |                                                                                                                                                                                                      
|32.1        | ** | Principal Executive Officer Certification and Principal Financial Officer Certification Pursuant
    to 18 U.S.C. Section 1350, as Adopted Pursuant to Section 906 of the Sarbanes-Oxley Act of 2002.
|            |    |                                                                                                                                                                                                      



*Exhibits filed herewith



** This exhibit shall not be deemed “filed” for purposes
of Section 18 of the Securities Exchange Act of 1934 or otherwise subject to the liabilities of the Section, nor shall it be deemed
incorporated by reference in any filings under the Security Act of 1933 or the Securities Exchange Act of 1934, whether made before
or after the date hereof and irrespective of any general incorporation language in any filing.



















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