In 1994, the third tier of German football underwent a reform which resulted in the elevation of the
Regionalliga. Wehen had finished seventh in the
Oberliga Hessen in the previous year and thus became a founding member of the
Regionalliga Süd. In spite of its relegation in 1995, the club managed to establish itself in the newly founded league over the next ten years. At the end of the
2006–07 season, Wehen finished first and earned promotion to the
2.Bundesliga. Its first second-tier season saw the club finish eighth and the inauguration of its current home,
Brita-Arena. In spite of a berth in the
DFB Pokal quarterfinals, Wehen was relegated to the
3. Liga in 2009, which would remain the club's division for the next ten seasons. Wehen achieved a third-place finish at the end of the
2018–19 season and thereby qualified for the promotion playoffs to the
2.Bundesliga against
FC Ingolstadt. After a 1–2 defeat in their home game, the team managed to carry a 3–2 victory on
Ingolstadt's turf. Advancing on away goals, Wehen was promoted to the 2. Bundesliga for only the second time in club history. However, the club experienced a difficult
2019–20 season and finished in 17th place, fielding the league's worst defence with 65 goals conceded. Along with
Dynamo Dresden, Wehen were relegated after just one season in the second tier. On 6 June 2023, Wehen Wiesbaden secured promotion to 2. Bundesliga from 2023 to 2024 after defeating Arminia Bielefeld on aggregate 6–1 in the promotion/relegation play-off matches and returned to the second tier after three years absence. ==Honours==