| 5. Round | 27/08/2016 | Rot-Weiß Erfurt | - | Fortuna Köln | 3:0 | ||||
| 7. Round | 17/09/2016 | Jahn Regensburg | - | Fortuna Köln | 2:2 | ||||
| 9. Round | 24/09/2016 | SG Sonnenhof Großaspach | - | Fortuna Köln | 2:3 |  |
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| 11. Round | 16/10/2016 | FSV Frankfurt | - | Fortuna Köln | 6:0 | ||||
| 12. Round | 22/10/2016 | Fortuna Köln | - | VfR Aalen | 0:2 | ||||
| 16. Round | 26/11/2016 | SC Paderborn 07 | - | Fortuna Köln | 1:1 | ||||
| 23. Round | 18/02/2017 | Holstein Kiel | - | Fortuna Köln | 5:1 | ||||
| 25. Round | 03/03/2017 | Chemnitzer FC | - | Fortuna Köln | 3:1 | ||||
| 26. Round | 11/03/2017 | Fortuna Köln | - | Jahn Regensburg | 2:2 | ||||
| 27. Round | 15/03/2017 | Hansa Rostock | - | Fortuna Köln | 1:1 | ||||
| 31. Round | 04/04/2017 | VfR Aalen | - | Fortuna Köln | 3:0 |
Germany