| 1. Round | 31/07/2016 | Werder Bremen II | - | Sportfreunde Lotte | 0:3 | ||||
| 2. Round | 05/08/2016 | Fortuna Köln | - | Werder Bremen II | 2:0 | ||||
| 4. Round | 13/08/2016 | SC Paderborn 07 | - | Werder Bremen II | 1:2 | ||||
| 5. Round | 26/08/2016 | Werder Bremen II | - | VfL Osnabrück | 4:2 | ||||
| 6. Round | 10/09/2016 | MSV Duisburg | - | Werder Bremen II | 1:0 | ||||
| 7. Round | 17/09/2016 | Werder Bremen II | - | 1. FSV Mainz 05 II | 2:1 | ||||
| 9. Round | 24/09/2016 | Preußen Münster | - | Werder Bremen II | 4:0 | ||||
| 10. Round | 01/10/2016 | Werder Bremen II | - | SV Wehen Wiesbaden | 0:1 |  |
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| 13. Round | 29/10/2016 | Chemnitzer FC | - | Werder Bremen II | 1:1 | ||||
| 24. Round | 24/02/2017 | VfL Osnabrück | - | Werder Bremen II | 0:1 | ||||
| 26. Round | 11/03/2017 | 1. FSV Mainz 05 II | - | Werder Bremen II | 0:1 | ||||
| 32. Round | 08/04/2017 | Werder Bremen II | - | Chemnitzer FC | 0:0 | ||||
| 33. Round | 15/04/2017 | Jahn Regensburg | - | Werder Bremen II | 3:1 | ||||
| 37. Round | 13/05/2017 | FSV Frankfurt | - | Werder Bremen II | 0:4 |
Germany