Basler joined FC Bayern Munich in 1996, where he won the Bundesliga title in 1997 and 1999, and scored the club's winning goal in the 1998 DFB-Pokal final. Basler also scored the opening goal for Bayern Munich in their 1999 UEFA Champions League Final against Manchester United at Camp Nou, Barcelona with a free-kick in the sixth minute of the game. Bayern went on to lose the match 2–1.