3. Liga 2008/09 Liga
| # | Team | Sp | S | U | N | Tore | Diff | Pkt | Form | Tend. |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 1. FC Union Berlin | 19 | 10 | 6 | 3 | 26:13 | +13 | 36:15 | – | |
| 2 | SC Paderborn 07 | 19 | 11 | 2 | 6 | 39:26 | +13 | 35:20 | – | |
| 3 | Fortuna Düsseldorf | 19 | 9 | 3 | 7 | 26:18 | +8 | 30:24 | – | |
| 4 | BSV Kickers Emden | 19 | 6 | 6 | 7 | 16:23 | -7 | 24:27 | – | |
| 5 | FC Bayern München II | 19 | 4 | 11 | 4 | 21:20 | +1 | 23:23 | – | |
| 6 | FC Erzgebirge Aue | 19 | 5 | 7 | 7 | 23:25 | -2 | 22:28 | – | |
| 7 | SpVgg Unterhaching | 19 | 6 | 4 | 9 | 27:35 | -8 | 22:31 | – | |
| 8 | SG Dynamo Dresden | 19 | 5 | 5 | 9 | 20:24 | -4 | 20:32 | – | |
| 9 | SV Sandhausen | 19 | 4 | 7 | 8 | 26:32 | -6 | 19:31 | – | |
| 10 | VfB Stuttgart II | 19 | 4 | 6 | 9 | 29:30 | -1 | 18:33 | – | |
| 11 | Kickers Offenbach | 19 | 3 | 9 | 7 | 15:21 | -6 | 18:30 | – | |
| 12 | FC Rot-Weiß Erfurt | 19 | 4 | 5 | 10 | 16:26 | -10 | 17:35 | – | |
| 13 | Wuppertaler SV | 19 | 3 | 8 | 8 | 12:22 | -10 | 17:32 | ▲ | |
| 14 | SSV Jahn Regensburg | 19 | 3 | 8 | 8 | 17:28 | -11 | 17:32 | ▼ | |
| 15 | FC Carl Zeiss Jena | 19 | 4 | 3 | 12 | 18:32 | -14 | 15:39 | ▲ | |
| 16 | Eintracht Braunschweig | 19 | 4 | 3 | 12 | 13:28 | -15 | 15:39 | ▼ | |
| 17 | SV Wacker Burghausen | 19 | 3 | 6 | 10 | 18:37 | -19 | 15:36 | ▼ | |
| 18 | SV Stuttgarter Kickers | 19 | 3 | 5 | 11 | 17:39 | -22 | 14:38 | – | |
| 19 | VfR Aalen | 19 | 2 | 6 | 11 | 14:37 | -23 | 12:39 | – | |
| 20 | SV Werder Bremen II | 19 | 2 | 4 | 13 | 15:32 | -17 | 10:43 | – |