| 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 | ||||
| 11. Round | 06/11/2016 | SV Merseburg 99 | - | Askania Bernburg | 2:0 | ||||
| 16. Round | 19/02/2017 | SV SCHOTT Jena | - | SV Merseburg 99 | 1:2 |  |
|||
| 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 | ||||
| 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 | ||||
| 27. Round | 14/05/2017 | SV Merseburg 99 | - | BSG Chemie Leipzig | 1:3 | ||||
| 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 | ||||
| 30. Round | 03/06/2017 | SV Merseburg 99 | - | Germania Halberstadt | 0:2 |
Germany