| 1. Round | 07/08/2016 | SV Merseburg 99 | - | SV SCHOTT Jena | 1:1 |  |
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| 2. Round | 13/08/2016 | SV SCHOTT Jena | - | VFC Plauen | 2:0 | ||||
| 3. Round | 28/08/2016 | Germania Halberstadt | - | SV SCHOTT Jena | 3:1 | ||||
| 4. Round | 10/09/2016 | SV SCHOTT Jena | - | Brandenburger SC Süd | 0:0 | |
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| 5. Round | 17/09/2016 | SV SCHOTT Jena | - | SSV Markranstädt | 2:1 | ||||
| 6. Round | 24/09/2016 | Bischofswerdaer FV | - | SV SCHOTT Jena | 0:0 | |
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| 7. Round | 01/10/2016 | SV SCHOTT Jena | - | VfL Halle 96 | 3:1 | |
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| 8. Round | 15/10/2016 | Inter Leipzig | - | SV SCHOTT Jena | 1:3 | ||||
| 9. Round | 22/10/2016 | SV SCHOTT Jena | - | FSV Barleben | 0:0 | ||||
| 14. Round | 03/12/2016 | Askania Bernburg | - | SV SCHOTT Jena | 1:1 | ||||
| 16. Round | 19/02/2017 | SV SCHOTT Jena | - | SV Merseburg 99 | 1:2 | |
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| 24. Round | 23/04/2017 | FSV Barleben | - | SV SCHOTT Jena | 2:1 | ||||
| 25. Round | 30/04/2017 | SV SCHOTT Jena | - | BSG Wismut Gera | 1:3 | ||||
| 26. Round | 07/05/2017 | Union Sandersdorf | - | SV SCHOTT Jena | 1:0 | ||||
| 27. Round | 12/05/2017 | SV SCHOTT Jena | - | FC Carl Zeiss Jena II | 1:2 | ||||
| 28. Round | 21/05/2017 | FC Einheit Rudolstadt | - | SV SCHOTT Jena | 2:1 | ||||
| 30. Round | 03/06/2017 | BSG Chemie Leipzig | - | SV SCHOTT Jena | 3:1 |
Germany