| 1. Round | 27/08/2016 | 1. FC Köln | - | SV Darmstadt 98 | 2:0 | ||||
| 5. Round | 25/09/2016 | 1. FC Köln | - | RB Leipzig | 1:1 | ||||
| 6. Round | 01/10/2016 | Bayern München | - | 1. FC Köln | 1:1 | ||||
| 7. Round | 15/10/2016 | 1. FC Köln | - | FC Ingolstadt 04 | 2:1 | ||||
| 8. Round | 22/10/2016 | Hertha BSC | - | 1. FC Köln | 2:1 | ||||
| 9. Round | 30/10/2016 | 1. FC Köln | - | Hamburger SV | 3:0 |  |
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| 11. Round | 19/11/2016 | Bor. Mönchengladbach | - | 1. FC Köln | 1:2 | |
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| 12. Round | 26/11/2016 | 1. FC Köln | - | FC Augsburg | 0:0 | ||||
| 13. Round | 03/12/2016 | 1899 Hoffenheim | - | 1. FC Köln | 4:0 | ||||
| 14. Round | 10/12/2016 | 1. FC Köln | - | Borussia Dortmund | 1:1 |  |
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| 15. Round | 17/12/2016 | Werder Bremen | - | 1. FC Köln | 1:1 | |
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| 16. Round | 21/12/2016 | 1. FC Köln | - | Bayer Leverkusen | 1:1 | ||||
| 18. Round | 28/01/2017 | SV Darmstadt 98 | - | 1. FC Köln | 1:6 | |
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| 23. Round | 04/03/2017 | 1. FC Köln | - | Bayern München | 0:3 | ||||
| 24. Round | 11/03/2017 | FC Ingolstadt 04 | - | 1. FC Köln | 2:2 | ||||
| 29. Round | 15/04/2017 | FC Augsburg | - | 1. FC Köln | 2:1 | ||||
| 31. Round | 29/04/2017 | Borussia Dortmund | - | 1. FC Köln | 0:0 | ||||
| 32. Round | 05/05/2017 | 1. FC Köln | - | Werder Bremen | 4:3 |
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