Mukherjee was a polyglot learned in Pali, French and Russian. Apart from his fellowships and memberships in several international academic bodies, he was recognised by an award of the title of "Saraswati" in 1910 from "pandits" in Nabadwip, followed by that of "Shastravachaspati" in 1912 from the Dhaka Saraswat Samaj, "Sambudhagama Chakravarty" in 1914 and "Bharat Martanda" in 1920. Mukherjee was appointed a Companion of the Order of the Star of India (CSI) in June 1909, and knighted in December 1911.