In 1883, Mukherjee topped the BA examination at Calcutta University to complete a postgraduate degree in mathematics. In 1883 S.N. Banerjee wrote an article in the newspaper "Bengalee" against the orders of the Calcutta High Court and he was arrested in contempt of court. Protests and "hartals" erupted across Bengal and other cities, led by a group of students headed by Mukherjee at Calcutta high court. In 1884, he won the Harishchandra Prize for academic achievements, and completed an M.A. with first-class honours in mathematics in 1885. In 1886, he was awarded a second Masters in Natural Sciences, making him the first student to be awarded a dual degree from Calcutta University. In the same year he was married to Jogomaya Devi, and also published his third mathematical paper, "A Note on Elliptic Functions." The paper was praised by the distinguished British mathematician and Fellow of the Royal Society Arthur Cayley as a contribution of "outstanding merit." Mukherjee was recognised for his achievements by the grant of the Premchand Roychand Fellowship in Mathematics and Physics, Pure and Applied. Still only aged 22, he was further recognised by his election as a Fellow of the Royal Society of Edinburgh (FRSE). By 1888, Mukherjee was a lecturer in mathematics for the recently established Indian Association for the Cultivation of Science (IACS).