Whaley made his film debut in 1987's "Ironweed". In 1989 he appeared in "Field of Dreams" and "Born on the Fourth of July". The latter film began a long collaboration with director Oliver Stone, including 1991's "The Doors", in which he played Robby Krieger, and, in the same year, "JFK", in which he played a conspirator in the JFK assassination. In 1990, Whaley appeared with Marlon Brando and Matthew Broderick in "The Freshman". In 1991, he starred in the John Hughes feature film "Career Opportunities".