3. Liga 2008/09 Liga
| # | Team | Sp | S | U | N | Tore | Diff | Pkt | Form | Tend. |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 1. FC Union Berlin | 38 | 22 | 12 | 4 | 59:23 | +36 | 78:24 | – | |
| 2 | Fortuna Düsseldorf | 38 | 20 | 9 | 9 | 54:33 | +21 | 69:36 | – | |
| 3 | SC Paderborn 07 | 38 | 20 | 8 | 10 | 68:38 | +30 | 68:38 | – | |
| 4 | SpVgg Unterhaching | 38 | 20 | 7 | 11 | 57:46 | +11 | 67:40 | – | |
| 5 | FC Bayern München II | 38 | 14 | 17 | 7 | 54:38 | +16 | 59:38 | – | |
| 6 | BSV Kickers Emden | 38 | 16 | 11 | 11 | 45:44 | +1 | 59:44 | – | |
| 7 | Kickers Offenbach | 38 | 12 | 16 | 10 | 40:35 | +5 | 52:46 | – | |
| 8 | SV Sandhausen | 38 | 12 | 14 | 12 | 58:52 | +6 | 50:50 | ▲ | |
| 9 | SG Dynamo Dresden | 38 | 13 | 11 | 14 | 46:46 | 0 | 50:53 | ▲ | |
| 10 | FC Rot-Weiß Erfurt | 38 | 13 | 11 | 14 | 46:48 | -2 | 50:53 | ▲ | |
| 11 | VfB Stuttgart II | 38 | 13 | 10 | 15 | 61:50 | +11 | 49:55 | ▼ | |
| 12 | FC Erzgebirge Aue | 38 | 12 | 12 | 14 | 43:43 | 0 | 48:54 | – | |
| 13 | Eintracht Braunschweig | 38 | 12 | 9 | 17 | 46:51 | -5 | 45:60 | – | |
| 14 | Wuppertaler SV | 38 | 11 | 12 | 15 | 36:45 | -9 | 45:57 | – | |
| 15 | SSV Jahn Regensburg | 38 | 11 | 12 | 15 | 37:51 | -14 | 45:57 | – | |
| 16 | FC Carl Zeiss Jena | 38 | 10 | 11 | 17 | 41:59 | -18 | 41:62 | ▲ | |
| 17 | SV Werder Bremen II | 38 | 10 | 10 | 18 | 49:58 | -9 | 40:64 | ▼ | |
| 18 | SV Wacker Burghausen | 38 | 10 | 10 | 18 | 40:65 | -25 | 40:64 | ▲ | |
| 19 | VfR Aalen | 38 | 8 | 15 | 15 | 38:60 | -22 | 39:60 | ▼ | |
| 20 | SV Stuttgarter Kickers | 38 | 7 | 11 | 20 | 38:71 | -33 | 32:71 | – |