Nelson earned a B.A. in philosophy from Swarthmore College in 1959. While there, he made an experimental humorous student film, The Epiphany of Slocum Furlow, in which the titular hero discovers the meaning of life. His contemporary at the college, musician and composer Peter Schickele, scored the film. Following a year of graduate study in sociology at the University of Chicago, Nelson began graduate work in philosophy at Harvard University in 1960, ultimately earning an A.M. in sociology from the Department of Social Relations in 1963. During his graduate studies, Nelson was a photographer and filmmaker at John C. Lilly's Communication Research Institute in Miami, Florida, where he briefly shared an office with Gregory Bateson. He began to neglect his formal studies and failed his doctoral comprehensive examination, ultimately precipitating his departure from Harvard. From 1964 to 1966, he was an instructor in sociology at Vassar College.