| 2. Round | 23/08/2008 | SC Freiburg II | - | SpVgg Greuther Fürth II | 1:3 |  |
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| 3. Round | 30/08/2008 | Waldhof Mannheim | - | SC Freiburg II | 3:2 | ||||
| 6. Round | 27/09/2008 | SC Freiburg II | - | 1. FC Heidenheim 1846 | 1:3 |  |
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| 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 | ||||
| 9. Round | 25/10/2008 | SV Wehen Wiesbaden II | - | SC Freiburg II | 0:3 | |
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| 10. Round | 29/10/2008 | SC Freiburg II | - | SpVgg Unterhaching II | 1:1 | ||||
| 11. Round | 02/11/2008 | Karlsruher SC II | - | SC Freiburg II | 0:0 | |
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| 12. Round | 08/11/2008 | SC Freiburg II | - | 1. FC Nürnberg II | 2:0 | ||||
| 13. Round | 15/11/2008 | SC Pfullendorf | - | SC Freiburg II | 5:0 | |
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| 15. Round | 29/11/2008 | 1. FC Eintracht Bamberg | - | SC Freiburg II | 2:0 | ||||
| 16. Round | 06/12/2008 | SC Freiburg II | - | TSV 1860 München II | 1:3 | ||||
| 17. Round | 13/12/2008 | Hessen Kassel | - | SC Freiburg II | 2:1 | |
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Germany