| 1. Round | 29/07/2016 | ZFC Meuselwitz | - | FC Carl Zeiss Jena | 0:2 |  |
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| 2. Round | 07/08/2016 | FC Carl Zeiss Jena | - | VfB Auerbach | 2:0 | ||||
| 3. Round | 10/08/2016 | FSV Budissa Bautzen | - | FC Carl Zeiss Jena | 0:1 | ||||
| 4. Round | 14/08/2016 | FC Carl Zeiss Jena | - | SV Babelsberg 03 | 3:0 | ||||
| 5. Round | 27/08/2016 | FC Carl Zeiss Jena | - | Union Fürstenwalde | 4:0 | ||||
| 8. Round | 23/09/2016 | Hertha BSC II | - | FC Carl Zeiss Jena | 0:3 |
Germany