3. Liga 2008/09 Liga
| # | Team | Sp | S | U | N | Tore | Diff | Pkt | Form | Tend. |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 1. FC Union Berlin | 36 | 22 | 11 | 3 | 56:19 | +37 | 77:20 | – | |
| 2 | SpVgg Unterhaching | 36 | 19 | 7 | 10 | 52:41 | +11 | 64:37 | ▲ | |
| 3 | Fortuna Düsseldorf | 36 | 18 | 9 | 9 | 51:32 | +19 | 63:36 | ▲ | |
| 4 | SC Paderborn 07 | 36 | 18 | 8 | 10 | 59:38 | +21 | 62:38 | ▼ | |
| 5 | FC Bayern München II | 36 | 14 | 15 | 7 | 51:35 | +16 | 57:36 | – | |
| 6 | BSV Kickers Emden | 36 | 15 | 10 | 11 | 42:42 | 0 | 55:43 | – | |
| 7 | Kickers Offenbach | 36 | 12 | 14 | 10 | 39:34 | +5 | 50:44 | – | |
| 8 | VfB Stuttgart II | 36 | 13 | 9 | 14 | 58:46 | +12 | 48:51 | – | |
| 9 | SV Sandhausen | 36 | 12 | 12 | 12 | 53:47 | +6 | 48:48 | – | |
| 10 | FC Rot-Weiß Erfurt | 36 | 13 | 9 | 14 | 43:45 | -2 | 48:51 | ▲ | |
| 11 | FC Erzgebirge Aue | 36 | 12 | 11 | 13 | 42:41 | +1 | 47:50 | ▼ | |
| 12 | SG Dynamo Dresden | 36 | 12 | 10 | 14 | 42:44 | -2 | 46:52 | – | |
| 13 | Eintracht Braunschweig | 36 | 12 | 8 | 16 | 43:46 | -3 | 44:56 | – | |
| 14 | SSV Jahn Regensburg | 36 | 10 | 12 | 14 | 34:48 | -14 | 42:54 | ▲ | |
| 15 | Wuppertaler SV | 36 | 10 | 11 | 15 | 33:43 | -10 | 41:56 | ▼ | |
| 16 | VfR Aalen | 36 | 8 | 15 | 13 | 36:56 | -20 | 39:54 | ▲ | |
| 17 | SV Werder Bremen II | 36 | 9 | 10 | 17 | 47:57 | -10 | 37:61 | ▲ | |
| 18 | FC Carl Zeiss Jena | 36 | 9 | 10 | 17 | 35:54 | -19 | 37:61 | ▼ | |
| 19 | SV Wacker Burghausen | 36 | 9 | 10 | 17 | 38:58 | -20 | 37:61 | ▼ | |
| 20 | SV Stuttgarter Kickers | 36 | 7 | 11 | 18 | 38:66 | -28 | 32:65 | – |