Professor Mukherjee's first work was done independently, while he was a MSc student of the Presidency College, his work on colloids was published in the Journal 
of the American Chemical Society in 1915. In 1919 he and Jnan Chandra Ghosh joined the University College, London to work in the Physical Chemistry Laboratory under the charge of Professor FG Donnan, FRS. Professor Mukherjee continued his research on colloids and his major line of work was to develop 
his theory of the electrokinetic double layer and its ionic constitution. JN Mukherjee's work on the electrochemistry of colloids is considered highly significant. He is also well known for the boundary method he developed for determining the cataphoretic speed of colloid particles.