| Pos. | Mannschaft | Tore |
|---|---|---|
| 1 | SC Paderborn | 68 |
| 2 | VfB Stuttgart II | 61 |
| 3 | 1. FC Union Berlin | 59 |
| 4 | SV Sandhausen | 58 |
| 5 | SpVgg Unterhaching | 57 |
| 6 | Fortuna Düsseldorf II | 54 |
| 7 | Bayern II | 54 |
| 8 | Werder Bremen II | 49 |
| 9 | Dynamo Dresden | 46 |
| 10 | Rot-Weiß Erfurt | 46 |
| 11 | Eintracht Braunschweig | 46 |
| 12 | Kickers Emden | 45 |
| 13 | Erzgebirge Aue | 43 |
| 14 | Carl Zeiss Jena | 41 |
| 15 | Kickers Offenbach | 40 |
| 16 | Wacker Burghausen | 40 |
| 17 | VfR Aalen | 38 |
| 18 | Stuttgarter Kickers | 38 |
| 19 | Jahn Regensburg | 37 |
| 20 | Wuppertaler SV | 36 |