After a talent scout caught her grade school performance in a Christmas play at the age of eight, she appeared on television in a few small roles. Her first significant role came when she was cast as Sam Jennings in The Safety of Objects (2001). Soon after that, she starred alongside Jodie Foster in the hit drama, Panic Room (2002) and was nominated for a Young Artist Award.
Praised for her Panic Room performance, she went on to join the cast of Cold Creek Manor (2003) as the daughter of Dennis Quaid and Sharon Stone. Though the film did not do well at the box office, she received another nomination for a Young Artist Award. After appearing in a handful of movies and a Showtime movie called Speak (2004), Stewart was cast in the role of a teenage singer living in a commune in Sean Penn's Into the Wild (2007), a critically acclaimed biopic. A third Young Artist Award nomination resulted in a win for this role. She also appeared in Mary Stuart Masterson's The Cake Eaters (2007) that same year.