Born in Lausanne, Chapuisat started his professional career with hometown club FC Lausanne-Sport, moving in January 1991 to Bundesliga's Bayer Uerdingen and switching to powerhouse Borussia Dortmund in that summer.

Chapuisat scored 20 league goals in his first season, two short of Torjäger Fritz Walter of the eventual champions VfB Stuttgart.

[1] He stayed with Borussia until 1999, conquering back-to-back titles – although he played sparingly in 1995–96 due to injuries – and adding the following campaign's UEFA Champions League, where he netted three in ten games during the victorious run.

[2] Chapuisat then transferred to Grasshopper Club Zürich, playing there for three years and helped them winning the league title in 2001.

[6] In the 1994 World Cup, appearing in four complete contests as the nation reached the round-of-16, he scored in a 4–1 win over Romania on 22 June.