In February 1967, he started working with Dudley Herschbach at Harvard University on reactions between hydrogen atoms and diatomic alkali molecules and the construction of a universal crossed molecular beams apparatus.  After the postdoctoral year with Herschbach he joined the University of Chicago faculty in 1968. In 1974, he returned to Berkeley as professor of chemistry and principal investigator at the Lawrence Berkeley National Laboratory, becoming a U.S. citizen the same year. Lee is a University Professor Emeritus of the University of California system.