| 2. Round | 05/08/2016 | FC Schalke 04 II | - | 1. FC Köln II | 0:1 |  |
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| 4. Round | 14/08/2016 | 1. FC Köln II | - | Sportfreunde Siegen | 1:1 | ||||
| 6. Round | 26/08/2016 | 1. FC Köln II | - | Rot-Weiß Oberhausen | 1:2 | |
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| 8. Round | 10/09/2016 | 1. FC Köln II | - | SC Wiedenbrück | 1:3 | ||||
| 9. Round | 17/09/2016 | Bonner SC | - | 1. FC Köln II | 2:3 | ||||
| 5. Round | 21/09/2016 | SG Wattenscheid 09 | - | 1. FC Köln II | 0:1 | |
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| 14. Round | 22/10/2016 | 1. FC Köln II | - | SV Rödinghausen | 0:3 | ||||
| 15. Round | 30/10/2016 | Rot Weiss Ahlen | - | 1. FC Köln II | 1:1 | ||||
| 3. Round | 19/11/2016 | 1. FC Köln II | - | Bor. Mönchengladbach II | 1:1 | ||||
| 18. Round | 26/11/2016 | Borussia Dortmund II | - | 1. FC Köln II | 2:1 | |
Germany