Mukherjee was born in Kolkata, West Bengal, India to a Bengali family. Her Bengali family had a rich cultural and musical heritage. She was introduced to music by her mother. She studied under Shri Susheel Banerjee, Ustad Mohammed Sagiruddin Khan, Pandit Chinmoy Lahiri, Pandit Laxman Prasad Jaipurwale, and Pandit Ramesh Nadkarni.