In 1992, Marcus began working as an assistant professor at Stanford University. He was promoted to associate professor in 1999, but left the next year for a professor position at Harvard University. He worked there until 2012, when he moved to the Niels Bohr Institute at the University of Copenhagen to serve as Villum Kahn Rasmussen Professor. He continues to hold his professorship in Copenhagen, but since 2023 has served as professor and Boeing Johnson Endowed Chair at the University of Washington. Marcus stated that he was "excited to shepherd exchange between the UW and University of Copenhagen" as he continues to hold appointments at both institutions.