Marušič has published extensively, and has supervised seven PhD students (as of 2013). He served as the third rector of the University of Primorska from 2011-2019, a university he lobbied to have established in his home town of Koper. His research focuses on topics in algebraic graph theory, particularly the symmetry of graphs and the action of finite groups on combinatorial objects. He is regarded as the founder of the Slovenian school of research in algebraic graph theory and permutation groups.