After becoming the last East German women's football champion in 1991, USV Jena was admitted to the Bundesliga after the reunification of Germany. They were relegated after one season and have remained in the 2nd tier league (then Regionalliga, later 2nd Bundesliga) since then. In 2003 Jena became champions of the northeastern Regionalliga but failed to achieve promotion to the Bundesliga. The decisive match was lost at home against Hamburger SV. A year later they qualified for the newly founded 2nd Bundesliga and were grouped into the southern division. In 2005 and 2006 they came in third, in 2007 even in second place. In the 2007–08 season, Jena finished first in the 2nd Bundesliga Süd and got promoted to the Bundesliga. In 2008–09 the managed a 9th place and improved to an 8th place the next season. The teams biggest success was reaching the final of the 2009–10 Frauen DFB-Pokal, where they lost 0–1 to FCR 2001 Duisburg.