3. Liga 2008/09 Liga
| # | Team | Sp | S | U | N | Tore | Diff | Pkt | Form | Tend. |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 1. FC Union Berlin | 34 | 20 | 11 | 3 | 53:19 | +34 | 71:20 | – | |
| 2 | SC Paderborn 07 | 34 | 18 | 7 | 9 | 56:33 | +23 | 61:34 | ▲ | |
| 3 | SpVgg Unterhaching | 34 | 18 | 7 | 9 | 50:40 | +10 | 61:34 | ▼ | |
| 4 | Fortuna Düsseldorf | 34 | 17 | 8 | 9 | 45:27 | +18 | 59:35 | – | |
| 5 | BSV Kickers Emden | 34 | 14 | 10 | 10 | 40:37 | +3 | 52:40 | – | |
| 6 | FC Bayern München II | 34 | 12 | 15 | 7 | 44:34 | +10 | 51:36 | – | |
| 7 | Kickers Offenbach | 34 | 12 | 12 | 10 | 38:33 | +5 | 48:42 | – | |
| 8 | SV Sandhausen | 34 | 12 | 11 | 11 | 51:44 | +7 | 47:44 | – | |
| 9 | FC Rot-Weiß Erfurt | 34 | 13 | 8 | 13 | 41:41 | 0 | 47:47 | ▲ | |
| 10 | FC Erzgebirge Aue | 34 | 12 | 10 | 12 | 42:40 | +2 | 46:46 | ▼ | |
| 11 | VfB Stuttgart II | 34 | 12 | 9 | 13 | 54:43 | +11 | 45:48 | ▲ | |
| 12 | Eintracht Braunschweig | 34 | 12 | 7 | 15 | 38:39 | -1 | 43:52 | ▼ | |
| 13 | SG Dynamo Dresden | 34 | 11 | 9 | 14 | 39:42 | -3 | 42:51 | – | |
| 14 | SSV Jahn Regensburg | 34 | 9 | 12 | 13 | 32:46 | -14 | 39:51 | – | |
| 15 | Wuppertaler SV | 34 | 9 | 11 | 14 | 32:41 | -9 | 38:53 | – | |
| 16 | FC Carl Zeiss Jena | 34 | 9 | 9 | 16 | 35:53 | -18 | 36:57 | – | |
| 17 | SV Wacker Burghausen | 34 | 9 | 9 | 16 | 35:53 | -18 | 36:57 | – | |
| 18 | VfR Aalen | 34 | 7 | 14 | 13 | 29:52 | -23 | 35:53 | – | |
| 19 | SV Werder Bremen II | 34 | 8 | 9 | 17 | 43:55 | -12 | 33:60 | – | |
| 20 | SV Stuttgarter Kickers | 34 | 7 | 10 | 17 | 37:62 | -25 | 31:61 | – |