He found first team opportunities few and far between at Winterthur, however, and joined FC St. Gallen a season later where he became a first team regular at the relatively young age of 24. St. Gallen were relegated from the Swiss Super League in 2002 but Stöckli did not go down with them as he joined newly promoted club AC Lugano.
Despite limited opportunities at Winterthur, Stöckli joined FC St. Gallen a year later and quickly became a regular starter for their first team at the age of 24. However, St. Gallen were relegated in 2002, but Stöckli remained with the club and moved to AC Lugano when they were promoted.