| 1. Round | 07/08/2016 | SV Merseburg 99 | - | SV SCHOTT Jena | 1:1 |  |
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| 2. Round | 12/08/2016 | SSV Markranstädt | - | SV Merseburg 99 | 1:2 | |
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| 3. Round | 28/08/2016 | SV Merseburg 99 | - | Bischofswerdaer FV | 3:1 | ||||
| 4. Round | 09/09/2016 | VfL Halle 96 | - | SV Merseburg 99 | 0:1 | ||||
| 5. Round | 18/09/2016 | SV Merseburg 99 | - | Inter Leipzig | 4:2 | |
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| 6. Round | 24/09/2016 | FSV Barleben | - | SV Merseburg 99 | 2:2 | ||||
| 7. Round | 02/10/2016 | SV Merseburg 99 | - | BSG Wismut Gera | 1:1 | ||||
| 8. Round | 14/10/2016 | Union Sandersdorf | - | SV Merseburg 99 | 1:1 | ||||
| 9. Round | 23/10/2016 | SV Merseburg 99 | - | FC Carl Zeiss Jena II | 2:2 | ||||
| 10. Round | 30/10/2016 | FC Einheit Rudolstadt | - | SV Merseburg 99 | 0:0 | ||||
| 11. Round | 06/11/2016 | SV Merseburg 99 | - | Askania Bernburg | 2:0 | |
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| 12. Round | 19/11/2016 | BSG Chemie Leipzig | - | SV Merseburg 99 | 2:0 | ||||
| 13. Round | 26/11/2016 | Brandenburger SC Süd | - | SV Merseburg 99 | 1:2 | ||||
| 14. Round | 04/12/2016 | SV Merseburg 99 | - | VFC Plauen | 2:1 | ||||
| 15. Round | 10/12/2016 | Germania Halberstadt | - | SV Merseburg 99 | 1:1 | ||||
| 16. Round | 19/02/2017 | SV SCHOTT Jena | - | SV Merseburg 99 | 1:2 |  |
Germany