| 1. Round | 07/08/2016 | SV Merseburg 99 | - | SV SCHOTT Jena | 1:1 | ||||
| 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 | |
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| 6. Round | 24/09/2016 | Bischofswerdaer FV | - | SV SCHOTT Jena | 0:0 | ||||
| 7. Round | 01/10/2016 | SV SCHOTT Jena | - | VfL Halle 96 | 3:1 | ||||
| 8. Round | 15/10/2016 | Inter Leipzig | - | SV SCHOTT Jena | 1:3 | ||||
| 9. Round | 22/10/2016 | SV SCHOTT Jena | - | FSV Barleben | 0:0 | ||||
| 10. Round | 30/10/2016 | BSG Wismut Gera | - | SV SCHOTT Jena | 1:0 | |
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| 11. Round | 05/11/2016 | SV SCHOTT Jena | - | Union Sandersdorf | 1:5 | ||||
| 12. Round | 19/11/2016 | FC Carl Zeiss Jena II | - | SV SCHOTT Jena | 3:0 | |
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| 13. Round | 26/11/2016 | SV SCHOTT Jena | - | FC Einheit Rudolstadt | 1:2 |  |
Germany