| 16. Round | 19/02/2017 | SV SCHOTT Jena | - | SV Merseburg 99 | 1:2 | ||||
| 18. Round | 04/03/2017 | Bischofswerdaer FV | - | SV Merseburg 99 | 5:0 | ||||
| 19. Round | 12/03/2017 | SV Merseburg 99 | - | VfL Halle 96 | 1:0 | ||||
| 17. Round | 26/03/2017 | SV Merseburg 99 | - | SSV Markranstädt | 0:0 | ||||
| 21. Round | 02/04/2017 | SV Merseburg 99 | - | FSV Barleben | 2:1 |  |
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| 22. Round | 08/04/2017 | BSG Wismut Gera | - | SV Merseburg 99 | 3:0 | ||||
| 23. Round | 16/04/2017 | SV Merseburg 99 | - | Union Sandersdorf | 2:1 | |
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| 24. Round | 22/04/2017 | FC Carl Zeiss Jena II | - | SV Merseburg 99 | 4:5 | ||||
| 20. Round | 26/04/2017 | Inter Leipzig | - | SV Merseburg 99 | 1:0 | ||||
| 25. Round | 30/04/2017 | SV Merseburg 99 | - | FC Einheit Rudolstadt | 0:2 | ||||
| 26. Round | 06/05/2017 | Askania Bernburg | - | SV Merseburg 99 | 3:1 | ||||
| 28. Round | 21/05/2017 | SV Merseburg 99 | - | Brandenburger SC Süd | 2:1 | ||||
| 29. Round | 28/05/2017 | VFC Plauen | - | SV Merseburg 99 | 1:4 | |
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| 30. Round | 03/06/2017 | SV Merseburg 99 | - | Germania Halberstadt | 0:2 |
Greece