She comes from a film-clan family of Bengali origin: Her father, Ram Mukherjee is a retired director. Her mother Krishna used to be a playback singer, while her brother Raja Mukherjee is a film producer. Her maternal aunt is Debashree Roy. Famous bollywood actress Kajol is her second cousin.
Besides acting in films, Mukerji also does many charity appearances for noble causes. Her most noteworthy show was Temptations 2005 where she performed in New Delhi. The event provided the opportunity to raise funds for National Centre For Promotional of Employment for Disabled People (NCPEDP), a leading disabled rights group. Shahrukh Khan and Priyanka Chopra were also amongst the many who contributed to this cause.
Mukerji celebrated her birthday in 2006, with the students of The Helen Keller Institute for the Deaf and Blind. She befriended the members of this Institute, when she was enacting her role of a blind and deaf girl in the movie Black. She thanked the students of the institute claiming she would not have been able to enact her performance in Black without them.
She has been closely associated with actors such as Govinda, Aamir Khan, Abhishek Bachchan and most recently, director Aditya Chopra in love affairs. Undeniably after some time, these link up have been regarded as rumours from both parties. Besides love affairs, she has been pitted against actress Preity Zinta over time and time again. Nonetheless, both actresses confirm a professional relationship between each other.
In 2006, the actress bought a new house for herself in Juhu. The interiors were done by Twinkle Khanna and it took an entire year to get ready.