After doing a short cameo appearance for the first time in her father's Bengali film Biyer Phool (1992), Mukerji made her acting debut four years later, as the protagonist of Raja Ki Aayegi Baraat (1996). Her performance as a rape victim in the film was well received, but when the film failed at the box office, she returned to college to complete her education.

Mukerji returned to films in 1998. Her first release that year was Ghulam, opposite Aamir Khan; the film did well at the box office. Karan Johar's directorial debut, Kuch Kuch Hota Hai, co-starring Shahrukh Khan and Kajol, followed for her that year. The movie was a blockbuster, and she received her first Filmfare Award in the Best Supporting Actress category.

She followed her career by signing on several projects. Unfortunately, most of them did not do well at the box office. Although Badal was one of the highest grossing films of 2000, she still didn't succeed to establish her status in the industry at that poin