| 13. Round | 06/11/2016 | SpVgg Erkenschwick | - | SC Paderborn 07 II | 0:0 | ||||
| 24. Round | 26/03/2017 | SC Paderborn 07 II | - | TuS Erndtebrück | 1:0 | ||||
| 26. Round | 09/04/2017 | SC Paderborn 07 II | - | Hammer SpVg | 1:2 | ||||
| 27. Round | 13/04/2017 | FCE Rheine | - | SC Paderborn 07 II | 2:1 | ||||
| 28. Round | 17/04/2017 | SC Paderborn 07 II | - | TSV Marl-Hüls | 6:0 |  |
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| 29. Round | 23/04/2017 | SC Hassel | - | SC Paderborn 07 II | 4:1 | ||||
| 30. Round | 30/04/2017 | SC Paderborn 07 II | - | SpVgg Erkenschwick | 3:0 | ||||
| 31. Round | 05/05/2017 | FC Gütersloh 2000 | - | SC Paderborn 07 II | 3:1 | ||||
| 32. Round | 14/05/2017 | SC Paderborn 07 II | - | Arminia Bielefeld II | 2:1 | ||||
| 33. Round | 20/05/2017 | SV Lippstadt 08 | - | SC Paderborn 07 II | 2:3 |
Switzerland