After completing a post-doctoral fellowship at the University of Reading in 1983, Marušič spent a year teaching high school mathematics in Koper. He worked for one year at the University of Minnesota Duluth as an assistant professor, and then spent three years at the University of California, Santa Cruz, from 1985-1988. In 1988, he returned to Slovenia to work at the University of Ljubljana, where he rose quickly through the ranks, becoming a full professor in 1994. He also held the post of vice-rector of student affairs there from 1989-1991. In 1991-92 he spent a year as a Fulbright scholar at the University of California, Santa Cruz.