The association collapsed in 1943 due to the pressures brought on by World War II, but was re-established after the conflict on 14 July 1947.

The club played host to Bundesliga giants Borussia Dortmund in a first round cup match, losing 3–0.

The club made a single season appearance in the Landesliga Bayern-Süd (V) in 1990–91 before returning to fifth-tier play in 2001, being relegated to the Bezirksoberliga Schwaben.

After a second place Landesliga result in 2007, Thannhausen advanced to the Bayernliga (IV) for the first time, winning the promotion round, becoming the 99th team to play in this league since 1963.

After two good seasons in the league, 2009–10 proved unsuccessful, with the team finishing 18th and being relegated back to the Landesliga.