After serving five terms as Vice-Chancellor of Calcutta University, Mukherjee declined to be reappointed to a sixth term in 1923 when the university's Chancellor, Governor of Bengal the Earl of Lytton, tried to impose conditions on his reappointment. Shortly thereafter, he also resigned his judgeship on the Calcutta High Court and resumed his private practice of law. While arguing a case in Patna the following year, Mukherjee died suddenly on 25 May 1924, a month before his sixtieth birthday. His body was returned to Kolkata and cremated at a funeral service which drew crowds of mourners.