| 1. Round | 14/08/2016 | SC Paderborn 07 II | - | SuS Neuenkirchen | 0:0 | ||||
| 2. Round | 21/08/2016 | TuS Ennepetal | - | SC Paderborn 07 II | 3:2 | ||||
| 4. Round | 04/09/2016 | 1. FC Kaan-Marienborn | - | SC Paderborn 07 II | 0:0 | ||||
| 5. Round | 11/09/2016 | ASC 09 Dortmund | - | SC Paderborn 07 II | 1:1 | ||||
| 6. Round | 18/09/2016 | SC Paderborn 07 II | - | SuS Stadtlohn | 0:2 | ||||
| 7. Round | 25/09/2016 | TuS Erndtebrück | - | SC Paderborn 07 II | 3:1 | ||||
| 8. Round | 02/10/2016 | SC Paderborn 07 II | - | Roland Beckum | 0:1 | ||||
| 9. Round | 09/10/2016 | Hammer SpVg | - | SC Paderborn 07 II | 2:1 | ||||
| 10. Round | 16/10/2016 | SC Paderborn 07 II | - | FCE Rheine | 0:0 | ||||
| 18. Round | 18/12/2016 | SuS Neuenkirchen | - | SC Paderborn 07 II | 1:1 | ||||
| 25. Round | 02/04/2017 | Roland Beckum | - | SC Paderborn 07 II | 2:3 | ||||
| 28. Round | 17/04/2017 | SC Paderborn 07 II | - | TSV Marl-Hüls | 6:0 | ||||
| 30. Round | 30/04/2017 | SC Paderborn 07 II | - | SpVgg Erkenschwick | 3:0 | ||||
| 32. Round | 14/05/2017 | SC Paderborn 07 II | - | Arminia Bielefeld II | 2:1 |  |
Germany