After graduating from American University with a degree in philosophy and religion, Fahey moved to California in 1963 to study philosophy at the University of California, Berkeley. Arriving on campus, Fahey, ever the outsider, began to feel dissatisfied with the program's curriculum. He later suggested that studying philosophy had been a mistake and that what he had wanted to understand was really psychology. He was equally unimpressed with Berkeley's post-Beat Generation, proto-hippie music scene, loathing in particular the Pete Seeger–inspired folk-music revivalists he found himself classed with. Eventually, Fahey moved south to Los Angeles to join UCLA's folklore master's program at the invitation of department head D. K. Wilgus, and received an M.A. in folklore in 1966. Fahey's master's thesis on the music of Charley Patton was later published by Studio Vista in 1970. He completed it with the musicological assistance of his friend Alan Wilson, who would go on to be in the band Canned Heat.