In July 2023, the Governor of West Bengal appointed him as the interim Vice-Chancellor of Rabindra Bharati University.

He joined the Calcutta High Court as an advocate in 1982 practicing mainly in civil and writ matters.

[4] In 2017, the Bar Council of Karnataka sought action against Mukherjee after he commented that Tipu Sultan was not a freedom fighter, but a monarch who fought to safeguard his interests.

On his retirement as chief justice, he was not accorded the customary farewell following a resolution passed by the Karnataka State Bar Council.

[8] Mukherjee's appointment by Governor C. V. Ananda Bose as the acting Vice-Chancellor of both Rabindra Bharati University and Presidency University took place amidst centre-state tensions between the governor and the Government of West Bengal.