| 2. Round | 05/08/2016 | Fortuna Köln | - | Werder Bremen II | 2:0 | ||||
| 4. Round | 13/08/2016 | Fortuna Köln | - | Holstein Kiel | 1:0 | ||||
| 7. Round | 17/09/2016 | Jahn Regensburg | - | Fortuna Köln | 2:2 |  |
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| 8. Round | 21/09/2016 | Fortuna Köln | - | Hansa Rostock | 0:2 | ||||
| 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 | ||||
| 24. Round | 25/02/2017 | Fortuna Köln | - | Rot-Weiß Erfurt | 0:1 | ||||
| 25. Round | 03/03/2017 | Chemnitzer FC | - | Fortuna Köln | 3:1 | ||||
| 38. Round | 20/05/2017 | 1. FSV Mainz 05 II | - | Fortuna Köln | 4:0 |
Germany