| Competition: | Regionalliga |
| Season: | 2006–07 |
| Promoted: | FC St. Pauli VfL Osnabrück SV Wehen TSG 1899 Hoffenheim |
| Relegated: | Holstein Kiel Borussia Mönchengladbach II Bayer Leverkusen II Hertha BSC II SV Wilhelmshaven 1. FC Saarbrücken SV Darmstadt 98 FK Pirmasens 1. FC Kaiserslautern II |
| Prevseason: | 2005–06 |
| Nextseason: | 2007–08 |
The 2006–07 Regionalliga season was the thirteenth 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, FC St. Pauli and SV Wehen, and the runners-up, VfL Osnabrück and TSG 1899 Hoffenheim, of every division were promoted to the 2. Bundesliga.
| Pl. | Player | Team | Goals |
|---|---|---|---|
| 1 | 17 | ||
| VfL Osnabrück | |||
| 3 | 15 | ||
| 4 | 14 | ||
| 5 | 13 | ||
| 6 | 12 | ||
| Wuppertaler SV Borussia | |||
| Kickers Emden | |||
| 9 | 11 | ||
| Dynamo Dresden | |||
| Rot Weiss Ahlen |
| Pl. | Player | Team | Goals |
|---|---|---|---|
| 1 | 17 | ||
| Stuttgarter Kickers (10) | |||
| TSG Hoffenheim (7) | |||
| 3 | 16 | ||
| SV Elversberg | |||
| 5 | 15 | ||
| 6 | 14 | ||
| TSG Hoffenheim | |||
| 8 | 12 | ||
| TSV 1860 München II | |||
| VfR Aalen |
'II' teams are amateur sides attached to higher league clubs and cannot be promoted above this level, irrespective of their final position.
In the event of a 'II' side finishing in the promotion places, the next club below will instead be promoted.