Siegenthaler obtained his trainer diplome at the German Sport University Cologne in 1978 and spent the Nationalliga 1979–80 season as player manager for Schaffhausen.
He was then manager for FC Laufen as they reached the second highest tier of the Swiss football league system for the first time in the club's history.
He acted as a youth coach for FC Grenchen and as trainer instructor for the Swiss Football Association.
In May 2005 he was appointed as Analyser for the Germany national team during the time when Jürgen Klinsmann was trainer.
Then as Joachim Löw was appointed chief coach, Siegenthalers contract as Chiefscout was prolonged.