Although Mukerji was born into the Mukherjee-Samarth family, in which her parents and relatives were members of the Indian film industry, she did not aspire to pursue a career in film. However, while still a teenager she dabbled with acting by playing a supporting role in her father's Bengali language film Biyer Phool (1996) and accepted a leading role in the 1996 social drama Raja Ki Aayegi Baraat on the insistence of her mother. She then began a full-time career in films and the 1998 action drama Ghulam was her first commercial success. She gained wider recognition for a supporting role in the romance Kuch Kuch Hota Hai (1998). The year 2002 marked a turning point for Mukerji when she was cast by Yash Raj Films as the star of the drama Saathiya.