Naughton attended Brown University and Yale Drama School. His acting career began when he appeared in a series of Broadway dramas and musicals. He has since become an accomplished actor in many supporting film and television roles.
His largest fame and notoriety has been in theater, however. He won the Theatre World Award for his performance in Long Day's Journey Into Night in 1971, and Tony Awards in 1990 and 1997. His films include The Paper Chase and The First Wives Club. He also starred with Ron Harper in the 1974 television series Planet of the Apes, a spin-off of the original movie. He has directed several plays in New York, including the 2002 revival of Thornton Wilder's Our Town, starring Paul Newman, which was filmed for cable TV in 2003. He also appears in cabarets. In 1997 he won critical acclaim with his portrayal of lawyer Billy Flynn in the musical Chicago, and in 2006 starred in the movie The Devil Wears Prada. In 2006, he played the part of Edie Sedgwick's father, Fuzzy Sedgwick in Factory Girl. He has appeared in television commercials promoting the drugs Cialis, Nexium and Nasalcrom.