| 1. Round | 29/07/2016 | MSV Duisburg | - | SC Paderborn 07 | 1:0 | ||||
| 5. Round | 27/08/2016 | SV Wehen Wiesbaden | - | SC Paderborn 07 | 1:2 | ||||
| 10. Round | 30/09/2016 | SC Paderborn 07 | - | Hansa Rostock | 0:3 | ||||
| 14. Round | 05/11/2016 | SC Paderborn 07 | - | VfR Aalen | 0:0 | ||||
| 23. Round | 18/02/2017 | Werder Bremen II | - | SC Paderborn 07 | 1:0 | ||||
| 28. Round | 18/03/2017 | SC Paderborn 07 | - | Jahn Regensburg | 0:2 |
Germany