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

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

|                                                               |
|---------------------------------------------------------------|
|                                                               |  |  |
| Ireland                                                       |   | 98-1111119 |
| (State or other jurisdiction ofincorporation or organization) |   | (I.R.S. EmployerIdentification Number) |

|                                                              |
|--------------------------------------------------------------|
|                                                              |  |  |
| Alexandra HouseThe Sweepstakes, BallsbridgeDublin 4, Ireland |
| (Address of principal executive offices including zip code)  |

|                                            |
|--------------------------------------------|
|                                            |  |  |
| Title of Each Class                        |   | Name of Each Exchange on Which Registered |
| Ordinary Shares, par value $0.01 per share |   | The NASDAQ Global Select Market |

----

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

|        |
|--------|
|        |
|   |

|        |
|--------|
|        |
|   |

----

|        |
|--------|
|        |  |  |  |  |
| Dated: | June 6, 2014 | Prothena Corporation plc(Registrant) |
|   |   |   |
|   |   | /s/ Dale B. Schenk |
|   |   | Dale B. Schenk |
|   |   | President and Chief Executive Officer |
|   |   |   |
|   |   | /s/ Tran B. Nguyen |
|   |   | Tran B. Nguyen |
|   |   | Chief Financial Officer |

----

|             |
|-------------|
|             |  |  |  |  |  |  |  |  |  |
|        |   |   |   | Previously Filed |   |
| ExhibitNo.  |   | Description |   | Form |   | File No. | Filing Date | Exhibit | Filed Herewith |
|        |   |   |   |   |   |   |   |   |   |
| 2.1         |   | Demerger Agreement, dated as of November 8, 2012 between Elan Corporation, plc and Prothena Corporation plc |   | 10/A |   | 001-35676 | 11/30/2012 | 2.1 |   |
|        |   |   |   |   |   |   |   |   |   |
| 2.2(a)      |   | Amended and Restated Intellectual Property License and Contribution Agreement, dated December 20, 2012, by and among Neotope Biosciences Limited, Elan Pharma International Limited, and Elan Pharmaceuticals, Inc. |   | 8-K |   | 001-35676 | 12/21/2012 | 2.1 |   |
|        |   |   |   |   |   |   |   |   |   |
| 2.2(b)      |   | Amendment Number One to the Amended and Restated Intellectual Property License and Contribution Agreement, retroactively effective December 20, 2012, by and among Neotope Biosciences Limited, Elan Pharma International Limited, Elan Pharmaceuticals, LLC, Elan Corporation, plc, and Crimagua Limited |   | S-1/A |   | 333-191218 | 9/30/2013 | 2.2(b) |   |
|        |   |   |   |   |   |   |   |   |   |
| 2.3         |   | Intellectual Property License and Conveyance Agreement, dated December 20, 2012, by and among Neotope Biosciences Limited, Elan Pharma International Limited and Elan Pharmaceuticals, Inc. |   | 8-K |   | 001-35676 | 12/21/2012 | 2.2 |   |
|        |   |   |   |   |   |   |   |   |   |
| 2.4         |   | Asset Purchase Agreement, dated December 20, 2012, between Elan Pharmaceuticals, Inc. and Prothena Biosciences Inc |   | 8-K |   | 001-35676 | 12/21/2012 | 2.3 |   |
|        |   |   |   |   |   |   |   |   |   |
| 3.1         |   | Amended and Restated Memorandum and Articles of Association of Prothena Corporation plc |   | 10-K |   | 001-35676 | 3/29/2013 | 3.1 |   |
|        |   |   |   |   |   |   |   |   |   |
| 4.1         |   | Reference is made to Exhibit 3.1 |   |   |   |   |   |   |   |
|        |   |   |   |   |   |   |   |   |   |
| 10.1(a)     |   | Tax Matters Agreement, dated December 20, 2012, by and between Elan Corporation, plc and Prothena Corporation plc |   | 8-K |   | 001-35676 | 12/21/2012 | 10.1 |   |
|        |   |   |   |   |   |   |   |   |   |
| 10.1(b)     |   | Amendment No. 1 to Tax Matters Agreement, dated June 25, 2013, by and between Elan Corporation, plc and Prothena Corporation plc |   | 10-Q |   | 001-35676 | 8/13/2013 | 10.2 |   |
|        |   |   |   |   |   |   |   |   |   |
| 10.2        |   | Transitional Services Agreement, dated December 20, 2012, by and between Elan Corporation, plc and Prothena Corporation plc |   | 8-K |   | 001-35676 | 12/21/2012 | 10.2 |   |
|        |   |   |   |   |   |   |   |   |   |
| 10.3        |   | Subscription and Registration Rights Agreement, dated as of November 8, 2012 by and among Prothena Corporation plc, Elan Corporation, plc and Elan Science One Limited |   | 10/A |   | 001-35676 | 11/30/2012 | 10.3 |   |
|        |   |   |   |   |   |   |   |   |   |
| 10.4† |   | License, Development, and Commercialization Agreement, dated December 11, 2013, by Neotope Biosciences Limited and Prothena Biosciences Inc with F. Hoffmann-La Roche Ltd. and Hoffmann-La Roche Inc. |   |   |   |   |   |   | X |
|        |   |   |   |   |   |   |   |   |   |

----

|             |
|-------------|
|             |  |  |  |  |  |  |  |  |  |
|        |   |   |   | Previously Filed |   |
| ExhibitNo.  |   | Description |   | Form |   | File No. | Filing Date | Exhibit | Filed Herewith |
|        |   |   |   |   |   |   |   |   |   |
| 10.5† |   | Master Process Development and Clinical Supply Agreement, dated as of June 23, 2010, as amended August 1, 2011, by and among Elan Pharma International Limited, Neotope Biosciences limited and Boehringer Ingelheim Pharma GmbH & Co. KG |   | 10-Q |   | 001-35676 | 8/13/2013 | 10.3 |   |
|        |   |   |   |   |   |   |   |   |   |
| 10.6        |   | Research and Development Services Agreement, dated December 20, 2012, by and between Elan Corporation, plc and Prothena Corporation plc |   | 8-K |   | 001-35676 | 12/21/2012 | 10.3 |   |
|        |   |   |   |   |   |   |   |   |   |
| 10.7#       |   | Form of Deed of Indemnity |   | 10/A |   | 001-35676 | 11/30/2012 | 10.5 |   |
|        |   |   |   |   |   |   |   |   |   |
| 10.8(a)     |   | Lease Agreement, dated as of March 18, 2010 between Are-San Francisco No. 33, LLC and Elan Pharmaceuticals, Inc. |   | 10/A |   | 001-35676 | 11/30/2012 | 10.6 |   |
|        |   |   |   |   |   |
| 10.8(b)     |   | First Amendment to Lease, dated as of November 18, 2011 between Are-San Francisco No. 33, LLC and Elan Pharmaceuticals, Inc. |   | 10/A |   | 001-35676 | 11/30/2012 | 10.7 |   |
|        |   |   |   |   |   |   |   |   |   |
| 10.8(c)     |   | Second Amendment to Lease, dated as of June 1, 2012 between Are-San Francisco No. 33, LLC and Elan Pharmaceuticals, Inc. |   | 10/A |   | 001-35676 | 11/30/2012 | 10.8 |   |
|        |   |   |   |   |   |   |   |   |   |
| 10.8(d)     |   | Third Amendment to Lease, dated as of October 3, 2012 between Are-San Francisco No. 33, LLC and Elan Pharmaceuticals, Inc. |   | 10/A |   | 001-35676 | 11/30/2012 | 10.9 |   |
|        |   |   |   |   |   |   |   |   |   |
| 10.8(e)     |   | Assignment of Tenant’s Interest in Lease and Assumption of Lease Obligations, dated as of December 2, 2012 between Elan Pharmaceuticals, Inc. and Prothena Biosciences Inc |   | 10/A |   | 001-35676 | 11/30/2012 | 10.10 |   |
|        |   |   |   |   |   |   |   |   |   |
| 10.8(f)     |   | Fourth Amendment to Lease, dated as of November 30, 2013 between ARE-San Francisco No. 33, LLC and Prothena Biosciences, Inc. |   | 8-K |   | 001-35676 | 12/05/2013 | 10.1 |   |
|        |   |   |   |   |   |   |   |   |   |
| 10.9#       |   | Prothena Corporation plc 2012 Long Term Incentive Plan |   | 8-K |   | 001-35676 | 12/21/2012 | 10.4 |   |
|        |   |   |   |   |   |   |   |   |   |
| 10.10#      |   | Prothena Biosciences Inc Amended and Restated Severance Plan |   | 10-K |   | 001-35676 | 3/29/2013 | 10.12 |   |
|        |   |   |   |   |   |   |   |   |   |
| 10.11#      |   | Prothena Corporation plc Incentive Compensation Plan |   | 8-K |   | 001-35676 | 12/21/2012 | 10.6 |   |
|        |   |   |   |   |   |   |   |   |   |
| 10.12       |   | License Agreement, dated as of December 31, 2008 between the University of Tennessee Research Foundation and Elan Pharmaceuticals, Inc. |   | 10/A |   | 001-35676 | 11/30/2012 | 10.14 |   |
|        |   |   |   |   |   |   |   |   |   |
| 10.13#      |   | Form of Deed of Indemnity for Former Officers and Directors |   | 10/A |   | 001-35676 | 12/13/2012 | 10.15 |   |
|        |   |   |   |   |   |   |   |   |   |
| 10.14#      |   | Employment Agreement, dated January 22, 2013, between Prothena Biosciences Inc and Dale B. Schenk |   | 8-K |   | 001-35676 | 1/25/2013 | 10.1 |   |
|        |   |   |   |   |   |   |   |   |   |

----

|            |
|------------|
|            |  |  |  |  |  |  |  |  |  |
|       |   |   |   | Previously Filed |   |
| ExhibitNo. |   | Description |   | Form |   | File No. | Filing Date | Exhibit | Filed Herewith |
|       |   |   |   |   |   |   |   |   |   |
| 10.15#     |   | Offer letter, dated March 20, 2013, between Prothena Biosciences Inc and Tran Nguyen |   | 8-K |   | 001-35676 | 3/28/2013 | 10.1 |   |
|       |   |   |   |   |   |   |   |   |   |
| 10.16#     |   | Offer letter, dated December 22, 2012, between Prothena Biosciences Inc and Gene Kinney |   | 10-K |   | 001-35676 | 3/29/2013 | 10.18 |   |
|       |   |   |   |   |   |   |   |   |   |
| 10.17#     |   | Offer letter, dated March 19, 2013, between Prothena Biosciences Inc and Martin Koller |   | 8-K |   | 001-35676 | 3/28/2013 | 10.2 |   |
|       |   |   |   |   |   |   |   |   |   |
| 10.18#     |   | Offer letter, dated December 14, 2012, between Prothena Biosciences Inc and Tara Nickerson |   | 10-K |   | 001-35676 | 3/29/2013 | 10.2 |   |
|       |   |   |   |   |   |   |   |   |   |
| 10.19#     |   | Offer letter, dated April 19, 2013, between Prothena Biosciences Inc and Karin L. Walker |   | 8-K |   | 001-35676 | 5/22/2013 | 10.1 |   |
|       |   |   |   |   |   |   |   |   |   |
| 21.1       |   | List of Subsidiaries |   | 10-K |   | 001-35676 | 3/7/2014 | 21.1 |   |
|       |   |   |   |   |   |   |   |   |   |
| 23.1       |   | Consent of KPMG LLP, independent registered public accounting firm |   | 10-K |   | 001-35676 | 3/7/2014 | 23.1 |   |
|       |   |   |   |   |   |   |   |   |   |
| 23.2       |   | Consent of independent registered public accounting firm, KPMG |   | 10-K |   | 001-35676 | 3/7/2014 | 23.2 |   |
|       |   |   |   |   |   |   |   |   |   |
| 24.1       |   | Power of Attorney(see signature page hereto) |   | 10-K |   | 001-35676 | 3/7/2014 | 24.1 |   |
|       |   |   |   |   |   |   |   |   |   |
| 31.1       |   | Certification of Principal Executive Officer pursuant to Rule 13a-14(a) and 15d-14(a) of the Securities Exchange Act of 1934, as adopted pursuant to Section 302 of the Sarbanes-Oxley Act of 2002 |   | 10-K |   | 001-35676 | 3/7/2014 | 31.1 |   |
|       |   |   |   |   |   |   |   |   |   |
| 31.2       |   | Certification of Principal Financial Officer pursuant to Rule 13a-14(a) and 15d-14(a) of the Securities Exchange Act of 1934, as adopted pursuant to Section 302 of the Sarbanes-Oxley Act of 2002 |   | 10-K |   | 001-35676 | 3/7/2014 | 31.2 |   |
|       |   |   |   |   |   |   |   |   |   |
| 31.3       |   | Certification of Principal Executive Officer pursuant to Rule 13a-14(a) and 15d-14(a) of the Securities Exchange Act of 1934, as adopted pursuant to Section 302 of the Sarbanes-Oxley Act of 2002 |   |   |   |   |   |   | X |
|       |   |   |   |   |   |   |   |   |   |
| 31.4       |   | Certification of Principal Financial Officer pursuant to Rule 13a-14(a) and 15d-14(a) of the Securities Exchange Act of 1934, as adopted pursuant to Section 302 of the Sarbanes-Oxley Act of 2002 |   |   |   |   |   |   | X |
|       |   |   |   |   |   |   |   |   |   |
| 32.1*      |   | Certification of Principal Executive Officer and Principal 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 |   | 001-35676 | 3/7/2014 | 32.1 |   |
|       |   |   |   |   |   |   |   |   |   |
| 32.2*      |   | Certification of Principal Executive Officer and Principal Financial Officer pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002 |   |   |   |   |   |   | X |
|       |   |   |   |   |   |   |   |   |   |

----

|            |
|------------|
|            |  |  |  |  |  |  |  |  |  |
|       |   |   |   | Previously Filed |   |
| ExhibitNo. |   | Description |   | Form |   | File No. | Filing Date | Exhibit | Filed Herewith |
|       |   |   |   |   |   |   |   |   |   |
| 101.INS+   |   | XBRL Instance Document |   | 10-K |   | 001-35676 | 3/7/2014 | 101 |   |
|       |   |   |   |   |   |   |   |   |   |
| 101.SCH+   |   | XBRL Taxonomy Extension Schema Document |   | 10-K |   | 001-35676 | 3/7/2014 | 101 |   |
|       |   |   |   |   |   |   |   |   |   |
| 101.CAL+   |   | XBRL Taxonomy Extension Calculation Linkbase Document |   | 10-K |   | 001-35676 | 3/7/2014 | 101 |   |
|       |   |   |   |   |   |   |   |   |   |
| 101.DEF+   |   | XBRL Taxonomy Extension Definition Linkbase Document |   | 10-K |   | 001-35676 | 3/7/2014 | 101 |   |
|       |   |   |   |   |   |   |   |   |   |
| 101.LAB+   |   | XBRL Taxonomy Extension Label Linkbase Document |   | 10-K |   | 001-35676 | 3/7/2014 | 101 |   |
|       |   |   |   |   |   |   |   |   |   |
| 101.PRE+   |   | XBRL Taxonomy Extension Presentation Linkbase Document |   | 10-K |   | 001-35676 | 3/7/2014 | 101 |   |

|   |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |
|---|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| * | Exhibit 32.1 and 32.2 are being furnished and shall not be deemed to be “filed” for purposes of Section 18 of the Securities Exchange Act of 1934, as amended (the “Exchange Act”), or otherwise subject to the liability of that section, nor shall such exhibit be deemed to be incorporated by reference in any registration statement or other document filed under the Securities Act of 1933, as amended, or the Exchange Act, except as otherwise specifically stated in such filing. |

|   |                                                                    |
|---|--------------------------------------------------------------------|
| # | Indicates management contract or compensatory plan or arrangement. |

|         |                                                                                                                                                                               |
|---------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| † | Portions of this exhibit (indicated by asterisks) have been omitted pursuant to a request for confidential treatment and this exhibit has been filed separately with the SEC. |

|   |                                                                                                                                                                                                                                                                                                                                                                                                                                        |
|---|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| + | XBRL information is furnished and not filed for purposes of Sections 11 and 12 of the Securities Act of 1933 and Section 18 of the Securities Exchange Act of 1934, and is not subject to liability under those sections, is not part of any registration statement or prospectus to which it relates and is not incorporated or deemed to be incorporated by reference into any registration statement, prospectus or other document. |