Following his Ph.D., Rothman did postdoctoral research with Harvey Lodish at Massachusetts Institute of Technology working on glycosylation of membrane proteins. He moved to the Department of Biochemistry at Stanford University in 1978. He was at Princeton University, from 1988 to 1991, before coming to New York to found the Department of Cellular Biochemistry and Biophysics at Memorial Sloan-Kettering Cancer Center, where he also served as vice-chairman of Sloan-Kettering Institute. In 2003, he left Sloan-Kettering to become a professor of physiology at Columbia University's College of Physicians and Surgeons and the head of Columbia's Center for Chemical Biology. He moved from Columbia to Yale in 2008, retaining a part-time appointment at Columbia. Since 2013 he is also holding a position as Distinguished Professor-in-Residence at the Shanghai Institute for Advanced Immunochemical Studies of ShanghaiTech University.
