McGaugh received his B.A. from San Jose State University in 1953 and his Ph.D. in psychology from the University of California, Berkeley, in 1959. He was briefly a professor at San Jose State and then did postdoctoral work in neuropharmacology with Nobel Laureate Professor Daniel Bovet at the
Istituto Superiore di Sanitá in Rome, Italy. He then became a professor at the University of Oregon from 1961 to 1964. He was recruited to the University of California, Irvine, in 1964 (the year of the school's founding) to be the founding chair of the Department of Psychobiology (now Neurobiology and Behavior). He became dean (1967–1970) of the School of Biological Sciences and Vice Chancellor (1975–1977) and executive Vice Chancellor (1978–1982) of the university. In 1982, he founded the Center for the Neurobiology of Learning and Memory and remained director from 1982 to 2004.