| Sa., 21.02.2009 | Holstein Kiel - 1. FC Magdeburg | 1:1 |
| Sa., 21.02.2009 | Hannover 96 II - FC Energie Cottbus II | 2:1 |
| So., 22.02.2009 | Hallescher FC - VfB Lübeck | 0:0 |
| Mi., 11.03.2009 | SV Babelsberg 03 - SV Wilhelmshaven | 4:0 |
| Mi., 18.03.2009 | FC Oberneuland 1948 - Türkiyemspor Berlin | 2:2 |
| Mi., 01.04.2009 | Chemnitzer FC - Altonaer FC 93 | 1:1 |
| Fr., 10.04.2009 | Hamburger SV II - FC Sachsen Leipzig | 4:0 |
| Mi., 15.04.2009 | Hertha BSC Berlin II - VFC Plauen | 1:0 |
| Mi., 22.04.2009 | FC Hansa Rostock II - VfL Wolfsburg II | 2:2 |
| Sp. | S-U-N | Tore | Diff. | P | ||||
|---|---|---|---|---|---|---|---|---|
| 1. |  |  | Holstein Kiel | 19 | 12-5-2 | 31:15 | 16 | 41 |
| 2. | |  | 1. FC Magdeburg | 19 | 12-4-3 | 30:14 | 16 | 40 |
| 3. | |  | Hallescher FC | 19 | 10-9-0 | 22:8 | 14 | 39 |
| 4. | |  | SV Babelsberg 03 | 18 | 9-8-1 | 20:8 | 12 | 35 |
| 5. | |  | SV Wilhelmshaven | 18 | 8-6-4 | 27:20 | 7 | 30 |
| 6. |  |  | Hannover 96 II | 19 | 8-3-8 | 26:24 | 2 | 27 |
| 7. |  |  | FC Hansa Rostock II | 18 | 8-2-8 | 31:28 | 3 | 26 |
| 8. | |  | VfL Wolfsburg II | 18 | 7-4-7 | 23:17 | 6 | 25 |
| 9. | |  | VFC Plauen | 18 | 6-6-6 | 25:25 | 0 | 24 |
| 10. | |  | Chemnitzer FC | 18 | 6-5-7 | 27:23 | 4 | 23 |
| 11. | |  | FC Oberneuland 1948 | 18 | 6-4-8 | 17:19 | -2 | 22 |
| 12. | |  | Altonaer FC 93 | 18 | 6-4-8 | 24:30 | -6 | 22 |
| 13. | |  | VfB Lübeck | 19 | 4-9-6 | 19:20 | -1 | 21 |
| 14. | |  | Türkiyemspor Berlin | 18 | 6-2-10 | 17:25 | -8 | 20 |
| 15. | |  | Hertha BSC Berlin II | 18 | 5-4-9 | 18:32 | -14 | 19 |
| 16. | |  | Hamburger SV II | 18 | 4-5-9 | 19:25 | -6 | 17 |
| 17. | |  | FC Sachsen Leipzig | 18 | 2-6-10 | 8:26 | -18 | 12 |
| 18. | |  | FC Energie Cottbus II | 19 | 1-4-14 | 11:36 | -25 | 7 |