3. Liga 2008/09 Liga
| # | Team | Sp | S | U | N | Tore | Diff | Pkt | Form | Tend. |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 1. FC Union Berlin | 37 | 22 | 12 | 3 | 57:20 | +37 | 78:21 | – | |
| 2 | Fortuna Düsseldorf | 37 | 19 | 9 | 9 | 53:33 | +20 | 66:36 | ▲ | |
| 3 | SC Paderborn 07 | 37 | 19 | 8 | 10 | 65:38 | +27 | 65:38 | ▲ | |
| 4 | SpVgg Unterhaching | 37 | 19 | 7 | 11 | 55:45 | +10 | 64:40 | ▼ | |
| 5 | FC Bayern München II | 37 | 14 | 16 | 7 | 53:37 | +16 | 58:37 | – | |
| 6 | BSV Kickers Emden | 37 | 15 | 11 | 11 | 42:42 | 0 | 56:44 | – | |
| 7 | Kickers Offenbach | 37 | 12 | 15 | 10 | 39:34 | +5 | 51:45 | – | |
| 8 | VfB Stuttgart II | 37 | 13 | 10 | 14 | 60:48 | +12 | 49:52 | – | |
| 9 | SV Sandhausen | 37 | 12 | 13 | 12 | 56:50 | +6 | 49:49 | – | |
| 10 | SG Dynamo Dresden | 37 | 13 | 10 | 14 | 45:45 | 0 | 49:52 | ▲ | |
| 11 | FC Rot-Weiß Erfurt | 37 | 13 | 10 | 14 | 44:46 | -2 | 49:52 | ▼ | |
| 12 | FC Erzgebirge Aue | 37 | 12 | 11 | 14 | 42:42 | 0 | 47:53 | ▼ | |
| 13 | Eintracht Braunschweig | 37 | 12 | 9 | 16 | 46:49 | -3 | 45:57 | – | |
| 14 | Wuppertaler SV | 37 | 11 | 11 | 15 | 34:43 | -9 | 44:56 | ▲ | |
| 15 | SSV Jahn Regensburg | 37 | 10 | 12 | 15 | 35:51 | -16 | 42:57 | ▼ | |
| 16 | SV Werder Bremen II | 37 | 10 | 10 | 17 | 49:57 | -8 | 40:61 | ▲ | |
| 17 | FC Carl Zeiss Jena | 37 | 10 | 10 | 17 | 39:57 | -18 | 40:61 | ▲ | |
| 18 | VfR Aalen | 37 | 8 | 15 | 14 | 37:58 | -21 | 39:57 | ▼ | |
| 19 | SV Wacker Burghausen | 37 | 9 | 10 | 18 | 38:64 | -26 | 37:64 | – | |
| 20 | SV Stuttgarter Kickers | 37 | 7 | 11 | 19 | 38:68 | -30 | 32:68 | – |