3. Liga 2008/09 Liga
| # | Team | Sp | S | U | N | Tore | Diff | Pkt | Form | Tend. |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 1. FC Union Berlin | 33 | 20 | 10 | 3 | 53:19 | +34 | 70:19 | – | |
| 2 | SpVgg Unterhaching | 33 | 18 | 6 | 9 | 49:39 | +10 | 60:33 | ▲ | |
| 3 | SC Paderborn 07 | 33 | 17 | 7 | 9 | 54:33 | +21 | 58:34 | ▼ | |
| 4 | Fortuna Düsseldorf | 33 | 16 | 8 | 9 | 44:27 | +17 | 56:35 | – | |
| 5 | BSV Kickers Emden | 33 | 14 | 9 | 10 | 39:36 | +3 | 51:39 | ▲ | |
| 6 | FC Bayern München II | 33 | 12 | 14 | 7 | 43:33 | +10 | 50:35 | ▼ | |
| 7 | Kickers Offenbach | 33 | 12 | 11 | 10 | 37:32 | +5 | 47:41 | – | |
| 8 | SV Sandhausen | 33 | 12 | 10 | 11 | 51:44 | +7 | 46:43 | ▲ | |
| 9 | FC Erzgebirge Aue | 33 | 12 | 10 | 11 | 42:37 | +5 | 46:43 | ▲ | |
| 10 | FC Rot-Weiß Erfurt | 33 | 13 | 7 | 13 | 40:40 | 0 | 46:46 | ▼ | |
| 11 | Eintracht Braunschweig | 33 | 12 | 7 | 14 | 37:36 | +1 | 43:49 | ▲ | |
| 12 | VfB Stuttgart II | 33 | 11 | 9 | 13 | 51:43 | +8 | 42:48 | ▼ | |
| 13 | SG Dynamo Dresden | 33 | 11 | 9 | 13 | 39:41 | -2 | 42:48 | ▼ | |
| 14 | SSV Jahn Regensburg | 33 | 9 | 11 | 13 | 31:45 | -14 | 38:50 | ▲ | |
| 15 | Wuppertaler SV | 33 | 9 | 10 | 14 | 31:40 | -9 | 37:52 | ▼ | |
| 16 | FC Carl Zeiss Jena | 33 | 9 | 9 | 15 | 35:51 | -16 | 36:54 | ▲ | |
| 17 | SV Wacker Burghausen | 33 | 9 | 8 | 16 | 34:52 | -18 | 35:56 | ▲ | |
| 18 | VfR Aalen | 33 | 7 | 14 | 12 | 28:49 | -21 | 35:50 | ▼ | |
| 19 | SV Werder Bremen II | 33 | 7 | 9 | 17 | 40:54 | -14 | 30:60 | – | |
| 20 | SV Stuttgarter Kickers | 33 | 6 | 10 | 17 | 34:61 | -27 | 28:61 | – |