| 10. Round | 23/10/2016 | Erzgebirge Aue | - | 1. FC Union Berlin | 1:3 | ||||
| 20. Round | 12/02/2017 | 1. FC Union Berlin | - | Arminia Bielefeld | 3:1 |  |
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| 23. Round | 03/03/2017 | 1. FC Union Berlin | - | Würzburger Kickers | 2:0 | ||||
| 24. Round | 10/03/2017 | FC St. Pauli | - | 1. FC Union Berlin | 1:2 | |
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| 33. Round | 14/05/2017 | 1. FC Union Berlin | - | 1. FC Heidenheim 1846 | 0:1 | ||||
| 34. Round | 21/05/2017 | SpVgg Greuther Fürth | - | 1. FC Union Berlin | 1:2 |
Austria