 From 1994 - 1998, Gilligan was Sports Director of SC Bern and then returned to the US to work as assistant coach for the hockey team of University of Massachusetts Amherst, the Massachusetts Minutemen and as a scout for NHL team Los Angeles Kings.For season 2005/06 he came back to Switzerland as head coach for NLA team Rapperswil-Jona Lakers.He is also the team's head coach for 2006/07 season.