| 2. Round | 13/08/2016 | FSV Barleben | - | FC Carl Zeiss Jena II | 1:2 | ||||
| 4. Round | 09/09/2016 | Union Sandersdorf | - | FC Carl Zeiss Jena II | 0:1 | ||||
| 7. Round | 02/10/2016 | Askania Bernburg | - | FC Carl Zeiss Jena II | 2:2 | ||||
| 8. Round | 16/10/2016 | FC Carl Zeiss Jena II | - | BSG Chemie Leipzig | 2:3 | ||||
| 11. Round | 04/11/2016 | Germania Halberstadt | - | FC Carl Zeiss Jena II | 0:1 |  |
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| 12. Round | 19/11/2016 | FC Carl Zeiss Jena II | - | SV SCHOTT Jena | 3:0 | ||||
| 20. Round | 19/03/2017 | FC Carl Zeiss Jena II | - | Brandenburger SC Süd | 5:2 | ||||
| 23. Round | 13/04/2017 | BSG Chemie Leipzig | - | FC Carl Zeiss Jena II | 1:1 | ||||
| 24. Round | 22/04/2017 | FC Carl Zeiss Jena II | - | SV Merseburg 99 | 4:5 | ||||
| 27. Round | 12/05/2017 | SV SCHOTT Jena | - | FC Carl Zeiss Jena II | 1:2 |
Germany