In 1910, he was appointed the President of the Imperial (now National) Library Council to which he donated his personal collection of 80,000 books which are arranged in a separate section. He was the president of the inaugural session of the Indian Science Congress in 1914. Mukherjee was a member of the 1917–1919 Sadler Commission, presided over by Michael Ernest Sadler, which inquired into the state of Indian education. He was thrice elected as the president of The Asiatic Society. Having served as a fellow and subsequently as a vice-president of the Indian Association for the Cultivation of Science since the 1890s, in 1922 he was elected President of the IACS and held the office until his death.