Mukerji was born in Calcutta (present-day Kolkata) on 21 March 1978. Her father, Ram Mukherjee (born to the Mukherjee-Samarth family), is a former film director and one of the founders of Filmalaya Studios. Her mother, Krishna Mukherjee, is a former playback singer. Her elder brother, Raja Mukherjee, is a film producer and director. Her maternal aunt, Debashree Roy, is a Bengali film actress and her paternal cousin, Kajol, is a Hindi film actress and her contemporary. Another paternal cousin, Ayan Mukerji, is a scriptwriter and film director. Despite her parents and most of her relatives being members of the Indian film industry, Mukerji was uninterested in pursuing a career in film. She said, "There were already too many actresses at home and I wanted to be someone different".