Whaley was born and raised in Syracuse, New York, the son of Robert W. Whaley, Sr. and Josephine (née Timilione). Whaley graduated from Anthony A. Henninger High School in 1981 and left home at 18. He graduated from the University at Albany.
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. Krieger himself reported that he was pleased with the way Whaley portrayed him. 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.
Over the next two years, he played supporting roles in movies such as Hoffa and Swing Kids. He appeared in his second leading film role in 1994's Swimming with Sharks. During the same year, he played a supporting role as the doomed Brett, who was memorably killed by Samuel L. Jackson's and John Travolta's characters in Pulp Fiction.

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