In November 1879, at the age of fifteen, Mukherjee passed the entrance exam of the Calcutta University in which he stood second and received a first grade scholarship. In the year 1880, he took admission at the Presidency College now (Presidency University) in Kolkata where he met P.C. Ray and Narendranath Dutta who would later become famous as Swami Vivekananda. Later that year, though only a first-year undergraduate, he published his first mathematical paper, on a new proof of the 25th proposition of Euclid's first book.