He joined FC Basel's first team for their 1957–58 season under manager Rudi Strittich.
In 1983 Ernst August Künnecke was hired as team coach for FC Basel and Emil Müller was appointed as his assistant.
Then during the 1984–85 season, Basel's club chairman Urs Gribi fired Künnecke following a league run of four defeats and six draws with only one win.
Gribi installed Müller as head coach up until the end of the season and he was able to lead the team away from the relegation zone.
[4] In 1989 Müller was appointed as manager for local club FC Münchenstein and remained here for three seasons.