| 18. Round | 20/12/2008 | SC Freiburg II | - | Viktoria Aschaffenburg | 1:3 | ||||
| 20. Round | 28/02/2009 | SC Freiburg II | - | Waldhof Mannheim | 1:0 | ||||
| 21. Round | 08/03/2009 | Eintracht Frankfurt II | - | SC Freiburg II | 1:2 | ||||
| 22. Round | 14/03/2009 | SC Freiburg II | - | SSV Reutlingen | 2:3 | ||||
| 23. Round | 21/03/2009 | 1. FC Heidenheim 1846 | - | SC Freiburg II | 5:1 | ||||
| 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 | ||||
| 26. Round | 18/04/2009 | SC Freiburg II | - | SV Wehen Wiesbaden II | 3:1 | ||||
| 28. Round | 02/05/2009 | SC Freiburg II | - | Karlsruher SC II | 1:0 | |
|||
| 29. Round | 09/05/2009 | 1. FC Nürnberg II | - | SC Freiburg II | 3:0 | ||||
| 30. Round | 12/05/2009 | SC Freiburg II | - | SC Pfullendorf | 4:2 | ||||
| 31. Round | 16/05/2009 | SSV Ulm 1846 | - | SC Freiburg II | 3:1 | ||||
| 32. Round | 23/05/2009 | SC Freiburg II | - | 1. FC Eintracht Bamberg | 5:0 | |
Germany