The club was formed in June 2002 as FC Wacker Tirol, and play their home games at Tivoli-Neu.

After finishing first in Regionalliga West (2002–03), Wacker advanced to Red Zac Erste Liga, and only a season later (2003–04) was promoted to Bundesliga.

One year later (2008) the club, now named FC Wacker Innsbruck, finished last and was relegated to the Austrian Football Second League.

After finishing runner-up in the 2008–09 season, FC Wacker Innsbruck won promotion back to the Austrian Bundesliga in 2010 in a tight run.

About 5000 Tyrolean supporters had travelled to the final away game on 28 May 2010 in Pasching against Red Bull Juniors, which FC Wacker Innsbruck won 2–0.