| 1. Round | 06/08/2016 | FC Carl Zeiss Jena II | - | Inter Leipzig | 0:4 | ||||
| 3. Round | 26/08/2016 | FC Carl Zeiss Jena II | - | BSG Wismut Gera | 1:3 | ||||
| 5. Round | 18/09/2016 | Brandenburger SC Süd | - | FC Carl Zeiss Jena II | 1:2 | ||||
| 6. Round | 24/09/2016 | FC Carl Zeiss Jena II | - | FC Einheit Rudolstadt | 1:2 | ||||
| 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 | ||||
| 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 | ||||
| 16. Round | 19/02/2017 | Inter Leipzig | - | FC Carl Zeiss Jena II | 0:0 | ||||
| 21. Round | 02/04/2017 | FC Einheit Rudolstadt | - | FC Carl Zeiss Jena II | 0:1 | ||||
| 22. Round | 08/04/2017 | FC Carl Zeiss Jena II | - | Askania Bernburg | 2:3 | ||||
| 25. Round | 28/04/2017 | VFC Plauen | - | FC Carl Zeiss Jena II | 0:0 | ||||
| 28. Round | 21/05/2017 | SSV Markranstädt | - | FC Carl Zeiss Jena II | 0:6 | ||||
| 29. Round | 29/05/2017 | Bischofswerdaer FV | - | FC Carl Zeiss Jena II | 3:0 |
Germany