As BSG Union Mühlhausen the team played most of the times in the Bezirksliga, the third level.

After a merger in 1994 with Fitniss 90, the team took the name SV 1899 Mühlhausen, in memory of the legendary club that played in the local football before World War II.

FC Germania, its predecessor was one of the founding members of the German Football Association (Deutscher Fussball Bund or German Football Association) at Leipzig in 1900.

SV 1899 remained active in football but plays at lower levels.

FC Union Mühlhausen won promotion to the tier six Thüringenliga in 2010 and has been playing at this level until 2016, achieving a third-place finish as its best result in 2013–14.