3. Liga 2008/09 Liga
| # | Team | Sp | S | U | N | Tore | Diff | Pkt | Form | Tend. |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 1. FC Union Berlin | 19 | 11 | 6 | 2 | 26:8 | +18 | 39:12 | – | |
| 2 | Fortuna Düsseldorf | 19 | 10 | 6 | 3 | 26:17 | +9 | 36:15 | – | |
| 3 | SpVgg Unterhaching | 19 | 11 | 2 | 6 | 31:20 | +11 | 35:20 | – | |
| 4 | FC Bayern München II | 19 | 8 | 6 | 5 | 30:18 | +12 | 30:21 | – | |
| 5 | SG Dynamo Dresden | 19 | 8 | 6 | 5 | 30:24 | +6 | 30:21 | – | |
| 6 | SC Paderborn 07 | 19 | 7 | 6 | 6 | 30:17 | +13 | 27:24 | ▲ | |
| 7 | SV Werder Bremen II | 19 | 7 | 6 | 6 | 24:23 | +1 | 27:24 | ▼ | |
| 8 | Wuppertaler SV | 19 | 7 | 6 | 6 | 18:17 | +1 | 27:24 | ▼ | |
| 9 | SV Sandhausen | 19 | 6 | 8 | 5 | 29:24 | +5 | 26:23 | ▼ | |
| 10 | SSV Jahn Regensburg | 19 | 7 | 5 | 7 | 18:21 | -3 | 26:26 | ▲ | |
| 11 | FC Erzgebirge Aue | 19 | 6 | 7 | 6 | 19:15 | +4 | 25:25 | ▼ | |
| 12 | BSV Kickers Emden | 19 | 6 | 6 | 7 | 21:27 | -6 | 24:27 | ▲ | |
| 13 | Kickers Offenbach | 19 | 5 | 8 | 6 | 15:17 | -2 | 23:26 | – | |
| 14 | VfB Stuttgart II | 19 | 6 | 4 | 9 | 26:26 | 0 | 22:31 | ▼ | |
| 15 | Eintracht Braunschweig | 19 | 6 | 4 | 9 | 23:28 | -5 | 22:31 | ▼ | |
| 16 | SV Wacker Burghausen | 19 | 5 | 6 | 8 | 16:27 | -11 | 21:30 | ▲ | |
| 17 | FC Rot-Weiß Erfurt | 19 | 4 | 8 | 7 | 19:28 | -9 | 20:29 | ▼ | |
| 18 | SV Stuttgarter Kickers | 19 | 5 | 4 | 10 | 14:29 | -15 | 19:34 | ▼ | |
| 19 | FC Carl Zeiss Jena | 19 | 4 | 5 | 10 | 17:31 | -14 | 17:35 | ▲ | |
| 20 | VfR Aalen | 19 | 4 | 5 | 10 | 21:36 | -15 | 17:35 | ▼ |