| 1. Round | 17/08/2008 | SC Freiburg | - | TSV 1860 München | 2:1 | ||||
| 3. Round | 01/09/2008 | SC Freiburg | - | Hansa Rostock | 1:0 |  |
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| 4. Round | 14/09/2008 | FC Augsburg | - | SC Freiburg | 1:3 | ||||
| 12. Round | 10/11/2008 | SC Freiburg | - | FC St. Pauli | 2:0 | ||||
| 13. Round | 16/11/2008 | FSV Frankfurt | - | SC Freiburg | 1:2 | ||||
| 18. Round | 01/02/2009 | TSV 1860 München | - | SC Freiburg | 0:2 | ||||
| 21. Round | 20/02/2009 | SC Freiburg | - | FC Augsburg | 1:0 | ||||
| 22. Round | 27/02/2009 | SV Wehen Wiesbaden | - | SC Freiburg | 0:1 | ||||
| 23. Round | 08/03/2009 | SC Freiburg | - | Alemannia Aachen | 2:1 | ||||
| 25. Round | 23/03/2009 | SC Freiburg | - | 1. FC Nürnberg | 0:1 | ||||
| 27. Round | 13/04/2009 | 1. FSV Mainz 05 | - | SC Freiburg | 1:2 | ||||
| 28. Round | 19/04/2009 | SC Freiburg | - | FC Ingolstadt 04 | 3:2 | ||||
| 29. Round | 24/04/2009 | FC St. Pauli | - | SC Freiburg | 1:2 | ||||
| 31. Round | 10/05/2009 | TuS Koblenz | - | SC Freiburg | 2:5 |
Germany