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.