Chabert made her start as young Cosette in Les Misérables on Broadway. Chabert was a member of the Broadway Kids which included Christy Carlson Romano, Chris Trousdale, and Greg Raposo. She was originally selected to play the role of "Young Lily" in the movie Return to the Blue Lagoon (1991), but bailed out for unknown reasons. Chabert became famous worldwide for her role as Claudia Salinger in the TV drama Party of Five, "I had to go through everything on that show—my first kiss, my first bra. I was 11 when it started," she said. She also gained fame for her portrayal of Penny Robinson in the 1998 movie based on the 1960s TV show Lost in Space.
Since 1998, she has been the voice of Eliza Thornberry in the animated series The Wild Thornberrys; she also voiced Eliza in two Wild Thornberrys movies, The Wild Thornberrys Movie (2002) and Rugrats Go Wild! (2003). She also provided the voice of Meg Griffin for the first production season of the animated sitcom Family Guy (1999), after which Mila Kunis took over the role. Chabert also had a role in The Brooke Ellison Story, a made-for-TV movie produced by Christopher Reeve, in which she played Brooke Ellison, based upon a real-life quadriplegic woman who overcame many obstacles to graduate from Harvard. She also starred in Daddy Day Care (2003), as Gretchen in Mean Girls (2004) and the made for TV movie Hello Sister, Goodbye Life (2006) on ABC Family. She appeared in a 2006 remake of the classic horror movie Black Christmas. She also performed the voice of Princess Elise from the game Sonic the Hedgehog for the PS3 and Xbox 360.
Chabert won the 2005 MTV Movie Award for Best On-Screen Team for Mean Girls, shared with Lindsay Lohan, Rachel McAdams, and Amanda Seyfried. She won both the 1997 and 1998 Hollywood Reporter's Annual YoungStar Award for Best Performance by a Young Actress in a Drama TV Series for Party of Five, and had been nominated three other times for work 1999-2000. The YoungStar awards honor the best film, TV and music performances made exclusively by 6 to 18 year olds and are voted on by the Hollywood Reporter readers.
Chabert was featured as cover girl of the January 2007 issue of Maxim.