In the 1990s the club was present mostly in regional leagues (third division) and were promoted to 2. Bundesliga in 2001. After three years they were relegated twice to fourth division but won, after being promoted to third division again, 3. Liga in 2009 to reach 2. Bundesliga. Union reached the final of the 2000–01 DFB-Pokal before losing 2–0 in the final in Berlin to Schalke 04. Union were promoted to the Bundesliga for the first time in their history in 2019, following a 2–2 aggregate draw in the Promotion-Relegation Playoff with VfB Stuttgart, which Union won on away goals.