Justin Whalin began working in theatre in his native San Francisco when he was about 11, performing in a touring company and then the San Francisco company of "The Little Prince". When he was 14, Clint Eastwood gave him a role in "The Drowning Pool" (1988) and Whalin was then lured to Hollywood to play Alan Quartermaine, Jr. on the ABC soap "General Hospital" for four months in 1987. In 1988, he landed a short-lived, recurring role as Scott Baio's truth- manipulating cousin on the syndicated sitcom, "Charles in Charge". Whalin then played Nick, the youngest son being raised by a widower father and a Latina housekeeper on "One of the Boys" (NBC, 1989).

Whalin began commuting between San Francisco and Los Angeles, making guest appearances on such series as "The Wonder Years", "Mr. Belvedere", "The Young Riders" and in the pilot for "Blossom". He made his TV-movie debut for the Disney Channel in "Perfect Harmony" (1991), which explored racism at a private boarding school. Having earned his high school equivalency diploma, he relocated to Los Angeles to play Craig T. Nelson's rebellious son in the miniseries "The Fire Next Time" (CBS, 1993). Also that year, he starred in two Schoolbreak Specials for CBS: "Crosses on the Lawn", in which he was a young man who gets involved in hate crimes, and "Other Mothers", in which he was a high school basketball player whose position on the team is jeopardized when the school discovers he is being raised by his natural mother and her lesbian partner. Whalin won a Daytime Emmy for his performance in the latter. He subsequently appeared as Robert Urich's eldest son in the short-lived CBS sitcom "It Had to Be You" (1993). The role of Jimmy Olson followed in the autumn of 1994, when Whalin replaced Michael Landes in the role.

Whalin has also appeared in feature films. His first lead came with "Child's Play 3" (1991), in which he was the youth plagued by a murderous doll at a military school. He was a porn-crazed teen pursued by the murderous Kathleen Turner in "Serial Mom" (1994) and had his first romantic lead as a troubled youth helped by an attractive teen angel in "Suzie Q" (1996).