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| Player | Team | Goals |
|---|---|---|
| S. Terodde | FC Cologne | 29 |
| J. Córdoba | FC Cologne | 20 |
| L. Hinterseer | VfL Bochum | 18 |
| F. Klos | Arminia Bielefeld | 17 |
| A. Wooten | SV Sandhausen | 17 |
| P. Klement | Paderborn | 16 |
| S. Adamyan | SSV Jahn Regensburg | 15 |
| P. Testroet | Erzgebirge Aue | 15 |
| A. Voglsammer | Arminia Bielefeld | 13 |
| R. Glatzel | 1. FC Heidenheim | 13 |
| P. Lasogga | Hamburger SV | 13 |
| M. Grüttner | SSV Jahn Regensburg | 12 |
| S. Andersson | Union Berlin | 12 |
| H. Al Ghaddioui | SSV Jahn Regensburg | 11 |
| S. Dursun | SV Darmstadt 98 | 11 |
| M. Schnatterer | 1. FC Heidenheim | 10 |
| T. Kempe | SV Darmstadt 98 | 10 |
| B. Tekpetey | Paderborn | 10 |
| C. Beck | 1. FC Magdeburg | 10 |
| S. Michel | Paderborn | 10 |
| C. Antwi-Adjej | Paderborn | 10 |
| S. Kittel | FC Ingolstadt 04 | 10 |
| J. Serra | Holstein Kiel | 10 |
| D. Keita-Ruel | SpVgg Greuther Fürth | 10 |
| F. Schleusener | SV Sandhausen | 10 |
| D. Drexler | FC Cologne | 9 |
| M. Koné | Dynamo Dresden | 9 |
| K. Wolze | MSV Duisburg | 9 |
| D. Lezcano | FC Ingolstadt 04 | 9 |
| T. Weilandt | VfL Bochum | 9 |