In 1943, Montroll was appointed as Head of the Mathematics Research Group at the Kellex Corporation in New York, working on programs associated with the Manhattan Project. In 1944 he went to the Polytechnic Institute of Brooklyn, as adjunct professor of chemistry, then in 1946 he returned to the University of Pittsburgh as assistant, and then associate, professor of physics and mathematics. During this time he also served as head of the Physics Branch of the Office of Naval Research from 1948 to 1950. In 1950 he was appointed as a research fellow at the Courant Institute in New York. In 1951 he was appointed Research Professor in the Institute for Fluid Dynamics and Applied Mathematics at the University of Maryland.