Marušič maintains his post at the University of Ljubljana, although he has also held an appointment at the University of Primorska since 2004, shortly after its founding. He has increasingly devoted his time to the newer university, where he established the Faculty of Mathematics, Natural Sciences, and Information Technologies (UP FAMNIT). He served as the dean of that faculty from 2007-2011. He was elected in 2011 as the third rector of the University of Primorska, a position which he held until 2019.