| 1. Round | 06/08/2016 | VfL Bochum | - | 1. FC Union Berlin | 2:1 |  |
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| 2. Round | 15/08/2016 | 1. FC Union Berlin | - | Dynamo Dresden | 2:2 | ||||
| 4. Round | 10/09/2016 | 1. FC Union Berlin | - | Karlsruher SC | 4:0 | ||||
| 5. Round | 16/09/2016 | TSV 1860 München | - | 1. FC Union Berlin | 1:2 |  |
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| 6. Round | 21/09/2016 | Würzburger Kickers | - | 1. FC Union Berlin | 0:1 | ||||
| 7. Round | 26/09/2016 | 1. FC Union Berlin | - | FC St. Pauli | 2:0 | ||||
| 8. Round | 30/09/2016 | 1. FC Nürnberg | - | 1. FC Union Berlin | 2:0 | ||||
| 12. Round | 05/11/2016 | 1. FC Kaiserslautern | - | 1. FC Union Berlin | 1:0 | ||||
| 15. Round | 05/12/2016 | 1. FC Union Berlin | - | Eintracht Braunschweig | 2:0 | ||||
| 16. Round | 09/12/2016 | 1. FC Heidenheim 1846 | - | 1. FC Union Berlin | 3:0 | ||||
| 25. Round | 20/03/2017 | 1. FC Union Berlin | - | 1. FC Nürnberg | 1:0 | ||||
| 27. Round | 05/04/2017 | 1. FC Union Berlin | - | Erzgebirge Aue | 0:1 | ||||
| 33. Round | 14/05/2017 | 1. FC Union Berlin | - | 1. FC Heidenheim 1846 | 0:1 |
Germany