| Competition: | Regionalliga |
| Season: | 2003–04 |
| Promoted: | Rot-Weiss Essen Dynamo Dresden FC Rot-Weiß Erfurt 1. FC Saarbrücken |
| Relegated: | SG Wattenscheid 09 FC Schalke 04 II FC Sachsen Leipzig VfR Neumünster 1. FC Schweinfurt 05 1. FC Eschborn 1. FC Kaiserslautern II |
| Prevseason: | 2002–03 |
| Nextseason: | 2004–05 |
The 2003–04 Regionalliga season was the tenth season of the Regionalliga tier three of the German football league system. It was contested in two geographical divisions with eighteen teams each. The competition began on 1 August 2003 with the first matches of each division and ended on the 5 June 2004.
| Pos | Player | Team | Goals |
|---|---|---|---|
| 1 |  Markus Feldhoff | KFC Uerdingen 05 | 22 |
| 2 |  Veselin Gerov | SC Paderborn 07 | 19 |
| Alexander Löbe | SG Wattenscheid 09 | 19 | |
| 3 |  Erwin Koen | Rot-Weiss Essen | 18 |
| 4 |  Daniel Teixeira | Holstein Kiel | 17 |
| 5 | Markus Katriniok | SG Wattenscheid 09 | 13 |
| Benjamin Köhler | Rot-Weiss Essen | 13 | |
 Abdul Iyodo | FC Schalke 04 | 13 | |
| Denis Koslov | Sachsen Leipzig | 13 | |
 Ahmet Kuru | Werder Bremen Amateure | 13 | |
| Pos | Player | Team | Goals |
|---|---|---|---|
| 1 |  Paolo Guerrero | Bayern Munich II | 21 |
| Zvjezdan Misimović | Bayern Munich II | 21 | |
| 2 | René Müller | Rot-Weiß Erfurt | 19 |
| 3 | Alexander Blessin | SC Pfullendorf | 16 |
 Neno Rogošić | VfR Aalen | 16 | |
| 4 | Ünal Demirkiran | VfR Aalen | 15 |
 Gunter Thiebaut | 1. FC Saarbrücken | 15 | |
| 5 |  John van Buskirk | Sportfreunde Siegen | 14 |
| 6 | Veselin Popovic | 1. FC Schweinfurt 05 | 13 |
| Mirnes Mesic | Stuttgarter Kickers | 13 | |
| Christian Seeber | VfR Aalen | 13 |