3. Liga 2008/09 Liga
| # | Team | Sp | S | U | N | Tore | Diff | Pkt | Form | Tend. |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | SC Paderborn 07 | 19 | 13 | 2 | 4 | 38:21 | +17 | 41:14 | – | |
| 2 | 1. FC Union Berlin | 19 | 11 | 6 | 2 | 33:15 | +18 | 39:12 | – | |
| 3 | BSV Kickers Emden | 19 | 10 | 5 | 4 | 24:17 | +7 | 35:17 | – | |
| 4 | Fortuna Düsseldorf | 19 | 10 | 3 | 6 | 28:16 | +12 | 33:21 | – | |
| 5 | SpVgg Unterhaching | 19 | 9 | 5 | 5 | 26:26 | 0 | 32:20 | ▲ | |
| 6 | FC Rot-Weiß Erfurt | 19 | 9 | 3 | 7 | 27:20 | +7 | 30:24 | ▲ | |
| 7 | Kickers Offenbach | 19 | 7 | 8 | 4 | 25:18 | +7 | 29:20 | ▲ | |
| 8 | FC Bayern München II | 19 | 6 | 11 | 2 | 24:20 | +4 | 29:17 | ▼ | |
| 9 | VfB Stuttgart II | 19 | 7 | 6 | 6 | 35:24 | +11 | 27:24 | – | |
| 10 | SV Sandhausen | 19 | 6 | 6 | 7 | 29:28 | +1 | 24:27 | – | |
| 11 | FC Carl Zeiss Jena | 19 | 6 | 6 | 7 | 24:28 | -4 | 24:27 | ▲ | |
| 12 | Eintracht Braunschweig | 19 | 6 | 5 | 8 | 23:23 | 0 | 23:29 | ▼ | |
| 13 | FC Erzgebirge Aue | 19 | 6 | 5 | 8 | 24:28 | -4 | 23:29 | ▼ | |
| 14 | VfR Aalen | 19 | 4 | 10 | 5 | 17:24 | -7 | 22:25 | ▼ | |
| 15 | SG Dynamo Dresden | 19 | 5 | 5 | 9 | 16:22 | -6 | 20:32 | ▲ | |
| 16 | SSV Jahn Regensburg | 19 | 4 | 7 | 8 | 19:30 | -11 | 19:31 | ▲ | |
| 17 | SV Wacker Burghausen | 19 | 5 | 4 | 10 | 24:38 | -14 | 19:34 | ▼ | |
| 18 | Wuppertaler SV | 19 | 4 | 6 | 9 | 18:28 | -10 | 18:33 | ▼ | |
| 19 | SV Werder Bremen II | 19 | 3 | 4 | 12 | 25:35 | -10 | 13:40 | ▲ | |
| 20 | SV Stuttgarter Kickers | 19 | 2 | 7 | 10 | 24:42 | -18 | 13:37 | ▼ |