His roles include Brett in Pulp Fiction, Robby Krieger in The Doors, Jim Dodge in Career Opportunities, young Archie "Moonlight" Graham in Field of Dreams, and Guy in Swimming with Sharks.
He has also appeared in films and TV series such as Born on the Fourth of July, The Freshman, A Midnight Clear, Swing Kids, Broken Arrow, Luke Cage, Red Dragon and World Trade Center.
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.
Whaley made his writing-directorial debut in his independent film Joe the King in 1999, featuring his Doors co-star Val Kilmer and longtime friend and colleague Ethan Hawke in starring roles.
Whaley's other film credits include Red Dragon, Rob the Mob, School of Rock, Broken Arrow, Little Monsters, A Midnight Clear, Janie Jones and I.Q.
His television credits include Gotham, The Blacklist, CSI, Curb Your Enthusiasm, Psych, Burn Notice, Ugly Betty, Mrs. Harris, When Trumpets Fade, Boston Legal, Medium, Blue Bloods, Bull, House, MacGyver, Divorce, Elementary, Under the Dome, the TV mini-series Madoff, Alcatraz and many others.