| 1. Round | 06/08/2016 | FC Carl Zeiss Jena II | - | Inter Leipzig | 0:4 | ||||
| 2. Round | 13/08/2016 | FSV Barleben | - | FC Carl Zeiss Jena II | 1:2 |  |
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| 3. Round | 26/08/2016 | FC Carl Zeiss Jena II | - | BSG Wismut Gera | 1:3 | ||||
| 4. Round | 09/09/2016 | Union Sandersdorf | - | FC Carl Zeiss Jena II | 0:1 | ||||
| 6. Round | 24/09/2016 | FC Carl Zeiss Jena II | - | FC Einheit Rudolstadt | 1:2 | ||||
| 7. Round | 02/10/2016 | Askania Bernburg | - | FC Carl Zeiss Jena II | 2:2 | |
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| 8. Round | 16/10/2016 | FC Carl Zeiss Jena II | - | BSG Chemie Leipzig | 2:3 | ||||
| 9. Round | 23/10/2016 | SV Merseburg 99 | - | FC Carl Zeiss Jena II | 2:2 | ||||
| 10. Round | 29/10/2016 | FC Carl Zeiss Jena II | - | VFC Plauen | 1:2 | ||||
| 12. Round | 19/11/2016 | FC Carl Zeiss Jena II | - | SV SCHOTT Jena | 3:0 | |
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| 13. Round | 26/11/2016 | FC Carl Zeiss Jena II | - | SSV Markranstädt | 4:0 | ||||
| 14. Round | 03/12/2016 | FC Carl Zeiss Jena II | - | Bischofswerdaer FV | 2:2 | |
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| 15. Round | 10/12/2016 | VfL Halle 96 | - | FC Carl Zeiss Jena II | 1:2 | |
Germany
Bosnia-Herzegovina