Whitaker began his professional acting career at the age of three by appearing in a television commercial for a local used car dealer. In 1965, Whitaker originated the character of the young Scotty Baldwin in the soap opera General Hospital. In 1966, he acted in a major feature film, The Russians Are Coming, the Russians Are Coming, which also starred Brian Keith, the actor who would later play Whitaker's uncle in the television series Family Affair.

Family Affair aired from 1966 to 1971. It co-starred Whitaker playing the role of an orphaned boy named Jody Davis, living in a high-rise apartment in New York City with his twin sister Buffy (Anissa Jones) and older sister Cissy (Kathy Garver), his bachelor uncle Bill Davis (Brian Keith), and Bill's gentleman's gentleman, Mr. French (Sebastian Cabot). While a regular on the show, Whitaker also starred in the Hallmark Hall of Fame production The Littlest Angel and an episode of the long-running western The Virginian in 1969.

After Family Affair, Whitaker went on to star in the 1973 Sid and Marty Krofft Saturday morning children's series Sigmund and the Sea Monsters alongside Billy Barty and Scott Kolden, as well as appeared in feature films, including Disney's Snowball Express (1972), The Biscuit Eater (1972), Napoleon and Samantha (1972), and The Magic Pony (1977). His most prominent feature film role during this period was the lead in the musical version of Tom Sawyer (1973).

Whitaker married Symbria Wright of Reseda, California, in 1984. She divorced him four years later to marry the friend who threw his bachelor party, which Whitaker says led him to abuse drugs and alcohol for nine years. He said, "that was what I called the precipitous event which caused me to lose faith in God and faith in myself and whatever else and kind of went to the dark side, Luke Skywalker. I started hanging out in bars and smoking marijuana and then going from marijuana to cocaine and methamphetamine and smoking heroin and losing three cars, four apartments, five jobs and a company that I'd started and ran into the ground."

Whitaker graduated from Sylmar High School, and then spent two years in Portugal doing missionary work for The Church of Jesus Christ of Latter-day Saints. Upon returning to the United States he attended Brigham Young University, graduating in 1986 with a degree in Communications. In an interview with Tom Snyder on The Late Late Show, Whitaker said he briefly worked as a computer consultant at CBS. He later joined a Los Angeles talent agency, Whitaker Entertainment, owned by his sister. Whitaker also was Dana Plato's manager.

In 1999, Whitaker received the Young Artist Former Child Star Lifetime Achievement Award at the 20th Youth in Film Awards.

Whitaker's family held an intervention and threatened not to have any more contact with him unless he got help for his substance abuse. He agreed and joined a twelve-step program. Whitaker ultimately became a certified drug counselor and founded a nonprofit organization for Spanish-speaking addicts. In 2011, he said that he had been clean and sober for 13 years.

In 2014, Whitaker starred as Judge Taylor in a theater production of To Kill a Mockingbird at Sandhills Community College in North Carolina.

In 2016, Whitaker gave a guest star cameo appearance in Amazon's reboot of Sigmund and the Sea Monsters. In the premiere episode, he played the part of a heckling boat owner Zach, against David Arquette's salty sea captain character, Captain Barnabas. The episode had a similar cameo appearance by original show creators, Sid and Marty Kroftt.