| 2. Round | 22/08/2008 | VfL Osnabrück | - | SC Freiburg | 2:2 | ||||
| 3. Round | 01/09/2008 | SC Freiburg | - | Hansa Rostock | 1:0 | ||||
| 5. Round | 21/09/2008 | SC Freiburg | - | SV Wehen Wiesbaden | 5:0 | ||||
| 6. Round | 28/09/2008 | Alemannia Aachen | - | SC Freiburg | 1:0 | ||||
| 7. Round | 03/10/2008 | SC Freiburg | - | MSV Duisburg | 2:0 | ||||
| 8. Round | 17/10/2008 | 1. FC Nürnberg | - | SC Freiburg | 2:0 | ||||
| 9. Round | 24/10/2008 | Rot Weiss Ahlen | - | SC Freiburg | 0:3 |  |
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| 10. Round | 29/10/2008 | SC Freiburg | - | 1. FSV Mainz 05 | 0:1 | ||||
| 21. Round | 20/02/2009 | SC Freiburg | - | FC Augsburg | 1:0 | ||||
| 24. Round | 15/03/2009 | MSV Duisburg | - | SC Freiburg | 2:0 | ||||
| 28. Round | 19/04/2009 | SC Freiburg | - | FC Ingolstadt 04 | 3:2 | ||||
| 29. Round | 24/04/2009 | FC St. Pauli | - | SC Freiburg | 1:2 | ||||
| 30. Round | 03/05/2009 | SC Freiburg | - | FSV Frankfurt | 4:1 | ||||
| 31. Round | 10/05/2009 | TuS Koblenz | - | SC Freiburg | 2:5 | ||||
| 32. Round | 13/05/2009 | SC Freiburg | - | SpVgg Greuther Fürth | 0:0 | ||||
| 34. Round | 24/05/2009 | SC Freiburg | - | 1. FC Kaiserslautern | 4:3 |
Germany