Mukherjee took her Madhyamik examination from Kamala Girls' High School. She studied for her higher secondary examinations from Patha Bhavan, Kolkata. She earned her Bachelor of Engineering degree from the department of computer science and technology of Bengal Engineering College under Calcutta University, Shibpur in 1987. She get a job at ORG Systems Private Ltd Kolkata as a system engineer. She earned her Master of Engineering degree from the department of computer science and engineering, Jadavpur University, in 1991. In 1996 she was awarded the prestigious Commonwealth scholarship for her PhD from the school of computer science at the University of Manchester, in the UK, finishing in 1999.