Johansson had her first significant screen breakthrough with her role as one of two orphaned teenaged sisters in Manny & Lo (1996), a coming-of-age drama directed by Lisa Krueger. Johansson, who shared the screen with Aleksa Palladino and Mary Kay Place, earned an Independent Spirit Award Best Actress nomination for her work in the film, and she soon found herself being tapped by Robert Redford to star as Kristin Scott Thomas' daughter in The Horse Whisperer (1998). Although the film met with a very mixed reception, Johansson was widely praised for her portrayal of a girl who loses her leg and her best friend in a horrific accident.

In 2000, the actress signed on to play one of the heroines (alongside Thora Birch) of Terry Zwigoff's screen adaptation of Ghost World, Daniel Clowes' celebrated comic about the adventures of two teen girls grappling with post-high school life. That same year, she starred in American Rhapsody, in which she portrayed a young girl who escapes communist Hungary in the 1950s and travels to the U.S.