| 3. Round | 30/08/2008 | Waldhof Mannheim | - | SC Freiburg II | 3:2 | ||||
| 7. Round | 04/10/2008 | TSV Großbardorf | - | SC Freiburg II | 2:0 |  |
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| 8. Round | 18/10/2008 | SC Freiburg II | - | SV Darmstadt 98 | 0:2 | ||||
| 14. Round | 22/11/2008 | SC Freiburg II | - | SSV Ulm 1846 | 1:1 | ||||
| 16. Round | 06/12/2008 | SC Freiburg II | - | TSV 1860 München II | 1:3 | |
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| 17. Round | 13/12/2008 | Hessen Kassel | - | SC Freiburg II | 2:1 | ||||
| 20. Round | 28/02/2009 | SC Freiburg II | - | Waldhof Mannheim | 1:0 |  |
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| 22. Round | 14/03/2009 | SC Freiburg II | - | SSV Reutlingen | 2:3 |  |
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| 23. Round | 21/03/2009 | 1. FC Heidenheim 1846 | - | SC Freiburg II | 5:1 | |
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| 24. Round | 28/03/2009 | SC Freiburg II | - | TSV Großbardorf | 3:0 | ||||
| 25. Round | 03/04/2009 | SV Darmstadt 98 | - | SC Freiburg II | 0:0 | ||||
| 27. Round | 26/04/2009 | SpVgg Unterhaching II | - | SC Freiburg II | 1:4 | ||||
| 31. Round | 16/05/2009 | SSV Ulm 1846 | - | SC Freiburg II | 3:1 |
Germany