In 1998 at the age of 18, she married singer Pramit Sen, son of Rabindra Sangeet singer exponent Sagar Sen. The marriage was unhappy, lasting two years before the couple separated. She accused him of physically abusing her and locking her out of their home when she was pregnant. She filed a charge against him for cruelty (it was later dismissed). According to Mukherjee, Sen filed for divorce in 2000, but changed his mind when she became successful in her acting career. She had one daughter from the marriage, Anwesha, born in 2000.
In 2001, Mukherjee enrolled at the Ananda Shankar Centre for Culture, learning dance from veteran Tanusree Shankar. Later, she began a relationship with Parambrata Chatterjee on the set of Brake Fail. As she was still lawfully married to Pramit Sen, he filed a charge against Chatterjee for Criminal adultery and enticement of a married woman. They separated in 2010 when Chatterjee moved to Bristol.
Mukherjee made her film debut in 2003 with the film Hemanter Pakhi, directed by Urmi Chakraborty. In this film she played a small role. Her first lead role came with Mastan, directed by Ravi Kinagi.
On 4 November 2014, she was caught on CCTV cameras tucking in a gold earring worth $255 (Rs.12,139) in her handbag at a jewellery showroom in a posh mall in Singapore. The shop owner filed a complaint against Mukherjee to the organizer of the film festival, but no police complaint was lodged against her. Mukherjee denied the charge and claimed that it might have happened "accidentally".
During the filming of Mastan, she began dating her co-star Jeet. They went on to appear in several films together, including Kranti, Krishnakanter Will and Partner. Mukherjee has recently appeared in Bye Bye Bangkok and made her Hindi debut in the anthology film Mumbai Cutting. She earned accolades for her cameo role in Detective Byomkesh Bakshy (2015).
