| 16. Round | 19/02/2017 | Inter Leipzig | - | FC Carl Zeiss Jena II | 0:0 | ||||
| 17. Round | 25/02/2017 | FC Carl Zeiss Jena II | - | FSV Barleben | 7:0 | ||||
| 19. Round | 11/03/2017 | FC Carl Zeiss Jena II | - | Union Sandersdorf | 2:3 | ||||
| 20. Round | 19/03/2017 | FC Carl Zeiss Jena II | - | Brandenburger SC Süd | 5:2 | ||||
| 18. Round | 26/03/2017 | BSG Wismut Gera | - | FC Carl Zeiss Jena II | 2:1 | ||||
| 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 | ||||
| 23. Round | 13/04/2017 | BSG Chemie Leipzig | - | FC Carl Zeiss Jena II | 1:1 |  |
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| 25. Round | 28/04/2017 | VFC Plauen | - | FC Carl Zeiss Jena II | 0:0 | ||||
| 26. Round | 06/05/2017 | FC Carl Zeiss Jena II | - | Germania Halberstadt | 0:4 | |
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| 28. Round | 21/05/2017 | SSV Markranstädt | - | FC Carl Zeiss Jena II | 0:6 | ||||
| 30. Round | 03/06/2017 | FC Carl Zeiss Jena II | - | VfL Halle 96 | 2:3 |
Germany