Ganguly was born in Kalyani near Kolkata, West Bengal, India. She grew up in a joint family.

Ganguly debuted in the Anil Kapoor starrer, Saaheb 1985, as a child actress. Her second role was in Malayalam film, Ithile Iniyum Varu (1986), with Mamoothy as lead. Though her first role as a lead actress, was the pivotal role of Draupadi, in B.R. Chopra's mythological TV series, Mahabharat (1988), which immediately got her attention , and also lead to a role in Mrinal Sen's, Ek Din Achanak (1989).

Her other notable works are in award-winning film, Padma Nadir Majhi (1993) by Gautam Ghose, Yugant (1995) by Aparna Sen, Abar Aranye (2003) by Gautam Ghose, Antarmahal (2006) by Rituparno Ghosh, apart from these film appearances she has done, numerous television series, both in Bengali and Hindi, including Sukanya (1998) etc.

After working in a few Hindi films, she shifted to Kolkata, and after appearing in numerous Bengali films through the 1990s, shifted based to Mumbai in 2007, with English film called, Bow Barracks Forever (2004), directed by Anjan Dutta , and continued to act in Bengali films. She started working in Hindi TV series, with Karam Apnaa Apnaa (2007), moving on to Love Story (SAB TV series) (2007), and more recently in Agle Janam Mohe Bitiya Hi Kijo (2009) .

Rupa Ganguly was married to Dhruba Mukherjee, a Mechanical Engineer, since 1992. After 14 years of marriage the couple separated in 2007, and later formally divorced in January 2009.. They have a son named Aakash.

She now lives with her boyfriend, Dibyendu, 13 years younger than her, in her Mumbai flat. Dibyendu is a singer. Her appearance in the concluding episode of STAR Plus's hit reality show, Sacch Ka Saamna (2009), the Indian adaptation of the British reality show, The Moment of Truth, created media stir

According to latest media news, Rupa has since split with Dibyendu who has now moved in with another Bengali film and TV actress Swastika.

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