| 1. Round | 31/07/2016 | 1. FC Magdeburg | - | Fortuna Köln | 0:3 | ||||
| 2. Round | 05/08/2016 | Fortuna Köln | - | Werder Bremen II | 2:0 | ||||
| 3. Round | 09/08/2016 | SV Wehen Wiesbaden | - | Fortuna Köln | 3:0 | ||||
| 4. Round | 13/08/2016 | Fortuna Köln | - | Holstein Kiel | 1:0 | ||||
| 7. Round | 17/09/2016 | Jahn Regensburg | - | Fortuna Köln | 2:2 | ||||
| 11. Round | 16/10/2016 | FSV Frankfurt | - | Fortuna Köln | 6:0 | ||||
| 12. Round | 22/10/2016 | Fortuna Köln | - | VfR Aalen | 0:2 | ||||
| 13. Round | 29/10/2016 | Sportfreunde Lotte | - | Fortuna Köln | 0:1 | ||||
| 14. Round | 05/11/2016 | Fortuna Köln | - | Preußen Münster | 0:1 | ||||
| 16. Round | 26/11/2016 | SC Paderborn 07 | - | Fortuna Köln | 1:1 | ||||
| 25. Round | 03/03/2017 | Chemnitzer FC | - | Fortuna Köln | 3:1 | ||||
| 30. Round | 01/04/2017 | Fortuna Köln | - | FSV Frankfurt | 0:0 |  |
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| 31. Round | 04/04/2017 | VfR Aalen | - | Fortuna Köln | 3:0 | ||||
| 36. Round | 06/05/2017 | VfL Osnabrück | - | Fortuna Köln | 1:2 | ||||
| 37. Round | 13/05/2017 | Fortuna Köln | - | MSV Duisburg | 0:3 | |
Germany