| 1. Round | 30/07/2016 | Jahn Regensburg | - | Hansa Rostock | 2:0 | ||||
| 2. Round | 05/08/2016 | Hansa Rostock | - | Preußen Münster | 1:0 | ||||
| 3. Round | 10/08/2016 | Hansa Rostock | - | SG Sonnenhof Großaspach | 0:0 | ||||
| 8. Round | 21/09/2016 | Fortuna Köln | - | Hansa Rostock | 0:2 | ||||
| 9. Round | 25/09/2016 | Hansa Rostock | - | FSV Zwickau | 5:0 |  |
|||
| 10. Round | 30/09/2016 | SC Paderborn 07 | - | Hansa Rostock | 0:3 | ||||
| 11. Round | 15/10/2016 | Hansa Rostock | - | VfL Osnabrück | 1:2 | |
|||
| 12. Round | 22/10/2016 | MSV Duisburg | - | Hansa Rostock | 0:1 | ||||
| 13. Round | 29/10/2016 | Hansa Rostock | - | 1. FSV Mainz 05 II | 1:1 |  |
|||
| 14. Round | 05/11/2016 | 1. FC Magdeburg | - | Hansa Rostock | 1:1 | ||||
| 15. Round | 19/11/2016 | Hansa Rostock | - | Werder Bremen II | 1:1 | ||||
| 16. Round | 25/11/2016 | SV Wehen Wiesbaden | - | Hansa Rostock | 1:1 | ||||
| 18. Round | 10/12/2016 | Rot-Weiß Erfurt | - | Hansa Rostock | 1:2 | |
|||
| 19. Round | 17/12/2016 | Hansa Rostock | - | Chemnitzer FC | 1:3 | ||||
| 20. Round | 28/01/2017 | Hansa Rostock | - | Jahn Regensburg | 0:0 | ||||
| 29. Round | 25/03/2017 | Hansa Rostock | - | SC Paderborn 07 | 1:1 | ||||
| 30. Round | 02/04/2017 | VfL Osnabrück | - | Hansa Rostock | 2:1 |
Germany