Weiler started his career 1990 with FC Winterthur, the club of his hometown, playing in the Challenge League. In 1993 he moved to FC Aarau who at the time were in the Swiss Super League. After only one season he changed sides with Servette FC, playing two seasons in Geneva and 41 games. From the 1996 season onwards, he played for FC Zürich for two seasons. He ended his career with his youth club FC Winterthur from 1998 to 2001. He retired in 2001.
Weiler became an assistant coach for Winterthur on 1 March 2001. He was interim head coach from June 2001 to July 2001 and from January 2002 to February 2002. He was head coach of St. Gallen between 9 October 2007 and 28 October 2007. Weiler became head coach of Aarau on 13 April 2011. He left Aarau on 21 May 2014. Weiler became the new head coach of 1. FC Nürnberg on 12 November 2014.