| Place | Player | Team | Goals | Penalties |
|---|---|---|---|---|
| 1. | Domi Kumbela | Eintracht Braunschweig | 19 | 5 |
| 1. | Patrick Mayer | 1. FC Heidenheim | 19 | 0 |
| 3. | Matthew Taylor | Rot Weiss Ahlen | 17 | 3 |
| 3. | Alexander Esswein | Dynamo Dresden | 17 | 0 |
| 5. | Olivier Occean | Kickers Offenbach | 16 | 1 |
| 5. | Dennis Kruppke | Eintracht Braunschweig | 16 | 1 |
| 7. | Bjorn Ziegenbein | Hansa Rostock | 14 | 0 |
| 8. | Eric Agyemang | Wacker Burghausen | 13 | 0 |
| 8. | Frank Loning | SV Sandhausen | 13 | 3 |
| 10. | Zlatko Janjic | SV Wehen Wiesbaden | 12 | 1 |
| 10. | Marc Schnatterer | 1. FC Heidenheim | 12 | 2 |
| 10. | Marcel Reichwein | Rot-Weiß Erfurt | 12 | 0 |
| 13. | Andreas Spann | 1. FC Heidenheim | 11 | 0 |
| 13. | Marcel Schied | Hansa Rostock | 11 | 0 |
| 15. | Marcus Steegmann | TuS Koblenz | 10 | 3 |
| 15. | Mohammed Lartey | Hansa Rostock | 10 | 0 |
| 15. | Sven Schipplock | VfB Stuttgart | 10 | 0 |
| 15. | Tino Semmer | Rot-Weiß Erfurt | 10 | 0 |
| 19. | Sebastian Hahnge | FC Carl Zeiss Jena | 9 | 0 |
| 19. | Abdenour Amachaibou | SpVgg Unterhaching | 9 | 0 |
| 19. | Tobias Janicke | Hansa Rostock | 9 | 0 |
| 19. | Tobias Schweinsteiger | Jahn Regensburg | 9 | 0 |
| 19. | Robert Lechleiter | VfR Aalen | 9 | 0 |
| 19. | Martin Dausch | VfR Aalen | 9 | 0 |
| 19. | Dani Schahin | Dynamo Dresden | 9 | 2 |
| 19. | Nils Pfingsten-Reddig | Rot-Weiß Erfurt | 9 | 8 |
| 27. | Giuseppe Pisano | 1. FC Saarbrücken | 8 | 0 |
| 27. | Karim Bellarabi | Eintracht Braunschweig | 8 | 0 |
| 27. | Nico Zimmermann | 1. FC Saarbrücken | 8 | 1 |
| 27. | Rudolf Zedi | Rot-Weiß Erfurt | 8 | 0 |
| 27. | Thomas Rathgeber | Kickers Offenbach | 8 | 1 |
| 32. | Tobias Rathgeb | VfB Stuttgart | 7 | 3 |
| 32. | Soufian Benyamina | VfB Stuttgart | 7 | 0 |
| 32. | Stephan Sieger | 1. FC Saarbrücken | 7 | 0 |
| 32. | Addy Menga | SV Wehen Wiesbaden | 7 | 0 |
| 32. | Markus Fuchs | 1. FC Saarbrücken | 7 | 0 |
| 32. | Marcus Piossek | Rot Weiss Ahlen | 7 | 0 |
| 32. | Radovan Vujanovic | Hansa Rostock | 7 | 0 |
| 39. | Pascal Testroet | Werder Bremen | 6 | 0 |
| 39. | Dominik Stroh-Engel | SV Babelsberg 03 | 6 | 1 |
| 39. | Marco Haller | Jahn Regensburg | 6 | 2 |
| 39. | Guido Kocer | SV Babelsberg 03 | 6 | 0 |
| 39. | Steffen Wohlfarth | Bayern Munich | 6 | 2 |
| 39. | Sebastian Hille | Rot Weiss Ahlen | 6 | 0 |
| 39. | Robert Koch | Dynamo Dresden | 6 | 0 |
| 39. | Damir Vrancic | Eintracht Braunschweig | 6 | 0 |
| 39. | Anton Makarenko | SV Babelsberg 03 | 6 | 0 |
| 39. | Marcel Ziemer | SV Wehen Wiesbaden | 6 | 0 |
| 39. | Deniz Yilmaz | Bayern Munich | 6 | 0 |
| 39. | Regis Dorn | SV Sandhausen | 6 | 0 |