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| Player | Team | Goals |
|---|---|---|
| M. Schäffler | SV Wehen | 22 |
| S. Michel | Paderborn | 19 |
| B. Girth | SV Meppen | 19 |
| S. Hain | SpVgg Unterhaching | 19 |
| P. Türpitz | 1. FC Magdeburg | 17 |
| F. Schleusener | Karlsruher SC | 17 |
| S. Andrist | SV Wehen | 15 |
| A. Grimaldi | Preußen Münster | 15 |
| D. Keita-Ruel | Fortuna Köln | 15 |
| C. Beck | 1. FC Magdeburg | 13 |
| D. Frahn | Chemnitzer FC | 13 |
| M. Morys | VfR Aalen | 13 |
| M. Ritter | Paderborn | 12 |
| O. Ademi | Würzburger Kickers | 12 |
| M. Slavov | Chemnitzer FC | 12 |
| S. Benyamina | Hansa Rostock | 11 |
| T. Thiele | FC Carl Zeiss Jena | 11 |
| R. König | FSV Zwickau | 11 |
| M. Kobylański | Preußen Münster | 10 |
| L. Schnellbacher | VfR Aalen | 10 |
| T. Röttger | SG Sonnenhof Grossaspach | 10 |
| B. Zolinski | Paderborn | 10 |
| H. Dahmani | Fortuna Köln | 10 |
| D. Srbeny | Paderborn | 9 |
| R. Kazior | Werder Bremen II | 9 |
| M. Heider | VfL Osnabrück | 9 |
| M. Oesterhelweg | Sportfreunde Lotte | 8 |
| A. Fink | Karlsruher SC | 8 |
| C. Antwi-Adjej | Paderborn | 8 |
| M. Álvarez | VfL Osnabrück | 8 |