The 2008–09 3. Liga was the inaugural season for the newly formed tier III of the German football league system. The inaugural game was played on 25 July 2008 between FC Rot-Weiß Erfurt and Dynamo Dresden, ending with a 1–0 win for Dresden. The last games were played on 23 May 2009. 1. FC Union Berlin were the inaugural champions, securing first place on 10 May 2009. Runners-up Fortuna Düsseldorf were also promoted. Third-placed team SC Paderborn 07 played a relegation/promotion play-off against the 16th-placed team from 2. Bundesliga, VfL Osnabrück, winning both games and earning promotion. Kickers Emden, VfR Aalen, and Stuttgarter Kickers were relegated to the Regionalliga.

Qualified teams

The following teams were relegated to 3. Liga from 2007–08 2. Bundesliga: The following teams qualified through Regionalliga North: The following teams qualified through Regionalliga South:

Teams, Head Coach, Cities and Stadiums

Managerial changes

League table

Results

Top scorers

Source: www.kicker.de