
Stiles's first film was a non-speaking part in I Love You, I Love You Not (1996), with Claire Danes and Jude Law. She also had small roles as Harrison Ford's daughter in Alan J. Pakula's The Devil's Own (1997) and in M. Night Shyamalan's Wide Awake (1998). Her first lead was in Wicked (1998), playing a teenage girl who might have murdered her mother so she could have her father all to herself. Critic Joe Balthai wrote she was "the darling of the 1998 Sundance Film Festival" and Internet movie writer Harry Knowles said she was the "discovery of the fest", but the film was not commercially released in the U.S. and went direct-to-video.
In 2001, after Stiles had become better known the role that gained Stiles renown was Kat Stratford, opposite Heath Ledger, in Gil Junger's 10 Things I Hate About You (1999), an adaptation of The Taming of the Shrew set in a high school in Tacoma, Washington. She won an MTV Movie Award for "Breakthrough Female Performance" for the role, and the Chicago Film Critics voted her the most promising new actress of the year. Foreign critics applauded her work as well, including Adina Hoffman, who praised her as "a young, serious looking Diane Lane" and Martin Hoyle, who commented that Stiles played Kat "with bloody-minded independent charm from the beginning with hints of wistfulness beneath the determination."

Stiles's next commercial success was in Save the Last Dance (2001), as an aspiring ballerina forced to leave her small town in downstate Illinois to live with her struggling musician father in Chicago after her mother dies in a car accident. At her new, nearly all-black school, she falls in love with the character played by Sean Patrick Thomas, who teaches her hip-hop dance steps that get her into The Juilliard School. The role won her two more MTV awards for "Best Kiss" and "Best Female Performance", and a Teen Choice Award for best fight scene for her battle with Bianca Lawson. Rolling Stone pronounced her "the coolest co-ed," putting her on the cover of its April 12, 2001 issue. She told Rolling Stone that she performed all her own dancing in the film, though the way the film was shot and edited might have made it appear otherwise.

Between the Bourne films, she appeared in Mona Lisa Smile (2003) as Joan, a student at Wellesley College in 1953, whose art professor (Julia Roberts) encourages her to pursue a career in law rather than become a wife and mother. Critic Stephen Holden referred to her as one of cinema's "brightest young stars," but the film met with generally unfavorable reviews.

In 2005, Stiles was cast opposite her Hamlet co-star Liev Schreiber in The Omen, a remake of the 1976 horror film. The film was released on June 6, 2006.
She returned to the Bourne series with a much larger role in The Bourne Ultimatum in 2007, and to this day it is her highest grossing film. Producer Lynda Obst said that Stiles was "turning into the next Meryl Streep." She will next work on a film adaptation of The Bell Jar, which coincidentally was a book her character was seen reading in her breakthrough film 10 Things I Hate About You. Stiles also appears in the forthcoming film Gospel Hill. She will act in the role of a woman who falls in love with her stalker in the upcoming thriller Cry of the Owl, based on the novel by Patricia Highsmith. In May 2010 was casted for a major role in Dexter.