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HSG Uni Jena, USV Jena, FF USV Jena

After becoming the last East German women's football champion in 1991, Uni 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 2004 a new women's club was founded, so the USV Jena became the FF USV Jena (FF for Frauenfußball, women's football)

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 team's biggest success was reaching the final of the 2009–10 Frauen DFB-Pokal, where they lost 0–1 to FCR 2001 Duisburg.^[]

From 1 July 2020 on, the club will play under a new name, after agreeing to a merger with the men's football club FC Carl Zeiss Jena.

Carl Zeiss's women's section

Carl Zeiss entered a women's team in the Thüringenliga, the 4th level, for the first time in the 2017/18 season. It remained in that league for three years, finishing first eventually. The team was created by transferring over USV Jena III. USV Jena kept their first two teams.

Merger with Carl Zeiss

After the 2019/20 season FF USV Jena, transferred all their teams to FC Carl Zeiss Jena, in order to combine forces and benefit of the larger club with its image.