While starring on "Home Improvement", Thomas began branching out into film work, In 1994, he gave a memorable if unseen performance in "The Lion King", lending his distinctive prepubescent raspy whisper to the film's young protagonist Simba. He made his feature film debut the following year in the comedy "Man of the House", a clunker starring Chevy Chase and Farrah Fawcett as a couple whose romance is derailed by her disagreeable son. Thomas veritably lit up the screen with a remarkable turn as the obnoxious but sympathetic young man, and was undoubtedly the one shining spot in an otherwise lackluster film. That same year he played Tom Sawyer to Brad Renfro's Huckleberry Finn in the lightweight adaptation "Tom and Huck". While the movie was less than impressive, the caliber of young talent onscreen was formidable, and the two magnetic child stars brought an interesting depth to their roles. "The Adventures of Pinocchio" followed in 1996, with Thomas playing the titular puppet-turned-boy in this forgettable live-action take on the classic tale. 1997 saw him take on the role of future nature photographer Marshall Stouffer in the fact-based adventure "Wild America", Here Thomas continued his work in wholesome fare, bringing a mixture of boyish exuberance and intensity to his part. He played a privileged prep school student on a mission to get home for the holidays to win back his girlfriend and be gifted with a Porsche in the teen-aimed comedy "I'll Be Home For Christmas" (1998).
1998 marked Thomas' final appearance on "Home Improvement", the actor departing from the show at the start of its final season in order to dedicate himself to his studies in the all-important junior year of high school. Fans who had watched Thomas grow from a wisecracking, charmingly hammy child performer to a thoughtful and obviously talented young man were sorry to see him go, but he would continue to act despite his increased concentration on education and began to shatter his boy-next-door stereotype with roles in gritty and challenging projects. Portraying a drug-addicted hustler in 1999's festival-screened independent "Speedway Junkie", Thomas surprised both his fans and critics with a strong and nuanced performance in a part far different from anything he has previously played. In 2000, amid rumors of his own homosexuality, the actor unflinchingly took on the role of a gay teenager tormented by his peers in the Terrence McNally-scripted drama "Mr. Roberts", a segment of the Showtime anthology "Common Ground". Thomas returned to the big screen with a turn as a menacing youth befriended by a Southern widow (Ellen Burstyn) in the independent "Walking Across Egypt" (2000) and reteamed with TV brother Zachary Ty Bryant as two of a group of five high-school students inexplicably kidnapped in the thriller "Held For Ransom" (lensed 1999).