| 1. Round | 16/08/2008 | SV Babelsberg 03 | - | VfB Lübeck | 1:0 | ||||
| 3. Round | 31/08/2008 | SV Babelsberg 03 | - | 1. FC Magdeburg | 2:0 | ||||
| 2. Round | 03/09/2008 | SV Wilhelmshaven | - | SV Babelsberg 03 | 1:1 |  |
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| 4. Round | 14/09/2008 | Energie Cottbus II | - | SV Babelsberg 03 | 0:1 | ||||
| 5. Round | 19/09/2008 | SV Babelsberg 03 | - | Altona 93 | 2:0 | ||||
| 6. Round | 26/09/2008 | Türkiyemspor Berlin | - | SV Babelsberg 03 | 0:2 | ||||
| 7. Round | 04/10/2008 | SV Babelsberg 03 | - | FC Oberneuland | 1:0 | ||||
| 15. Round | 28/11/2008 | VfL Wolfsburg II | - | SV Babelsberg 03 | 0:2 | ||||
| 12. Round | 03/12/2008 | SV Babelsberg 03 | - | Hallescher FC | 0:2 | ||||
| 17. Round | 14/12/2008 | Sachsen Leipzig | - | SV Babelsberg 03 | 0:0 | ||||
| 18. Round | 20/12/2008 | VfB Lübeck | - | SV Babelsberg 03 | 1:1 |
Germany