| Competition: | Regionalliga |
| Season: | 2005–06 |
| Promoted: | Rot-Weiss Essen FC Carl Zeiss Jena FC Augsburg TuS Koblenz |
| Relegated: | SC Preußen Münster SG Wattenscheid 09 Rot-Weiß Oberhausen 1. FC Köln II Chemnitzer FC SpVgg Bayreuth SV Eintracht Trier 05 SSV Jahn Regensburg 1. FC Eschborn |
| Prevseason: | 2004–05 |
| Nextseason: | 2006–07 |
The 2005–06 Regionalliga season was the twelfth season of the Regionalliga at tier three of the German football league system. It was contested in two geographical divisions with eighteen teams in the south and nineteen in the north. The champions, Rot-Weiss Essen and FC Augsburg, and the runners-up, FC Carl Zeiss Jena and TuS Koblenz, of every division were promoted to the 2. Bundesliga.
1Eintracht Braunschweig were promoted due to VfB Lübeck being barred from promotion.
4Despite being champions of Oberliga Südwest, Borussia Neunkirchen were barred from promotion. Instead, 1. FC Kaiserslautern II was promoted to the Regionalliga Süd.
| Pos | Player | Team | Goals |
|---|---|---|---|
| 1 |  Thomas Reichenberger | VfL Osnabrück | 17 |
| 2 | Marcus Feinbier | Fortuna Düsseldorf | 15 |
| Sebastian Hähnge | FC Carl Zeiss Jena | 15 | |
| 3 | Marcel Podszus | Fortuna Düsseldorf | 14 |
| Lars Toborg | SG Wattenscheid 09 | 14 | |
| 4 | Danko Boskovic | Rot-Weiss Essen | 13 |
 Massimo Cannizzaro | Kickers Emden | 13 | |
| Timo Röttger | Bayer Leverkusen II | 13 | |
| 5 |  Daniel Chitsulo | 1. FC Köln II | 12 |
| Ashkan Dejagah | Hertha BSC II | 12 | |
| Pavel Dobry | Holstein Kiel | 12 | |
| Dirk Heinzmann | Wuppertaler SV | 12 |
| Pos | Player | Team | Goals |
|---|---|---|---|
| 1 |  Maximilian Nicu | SV Wehen | 16 |
 Christian Okpala | FC Augsburg | 16 | |
| 2 |  Salif Keita | TuS Koblenz | 15 |
| Bakary Diakité | SV Wehen | 15 | |
| Bernd Nehrig | VfB Stuttgart II | 15 | |
| 3 | Enrico Kern | Jahn Regensburg | 14 |
| 4 |  Najeh Braham | Eintracht Trier | 12 |
 Matias Cenci | SV Darmstadt 98 | 12 | |
 Elton Da Costa | FC Augsburg | 12 | |
 Mikheil Sajaia | SpVgg Bayreuth | 12 | |
| 5 | Nicky Adler | TSV 1860 München II | 11 |
| Martin Driller | SpVgg Bayreuth | 11 | |
| Anel Džaka | TuS Koblenz | 11 |