Fuller attended Regis High School in Manhattan. Admitted as a John Jay Scholar to Columbia University, he majored in History and Sociology and graduated summa cum laude in 1979. Awarded a Kellett Fellowship, he studied at Clare College, Cambridge, and received an M.Phil. in History and Philosophy of Science in 1981. He earned his Ph.D. in the same subject from the University of Pittsburgh in 1985, where he was an Andrew Mellon Pre-Doctoral Fellow. Fuller's doctoral dissertation, "Bounded Rationality in Law and Science", explored the implications of the views of Herbert A. Simon for political theory and philosophy of science.