From the Municipal high School, Burdwan, Mukherjee appeared in March 1909 at the last Entrance Examination of the Calcutta University and got a District Scholarship. Jnanendra Nath was a student of Presidency College (1909–1915) and received his BSc (1913) and MSc (1915) degrees from the Rajabazar Science College, Calcutta University. 
Based on his thesis for MSc Degree a paper on Electric Synthesis of Colloids was published in the Journal of the American Chemical Society (1915,39,292).