Nagchaudhuri's research focused on nuclear isomers, induced radioactivity, Cherenkov radiation and nonthermal plasma. During his doctorate at Berkeley, he had worked with the pioneers of the cyclotron. Before returning to India in 1941, with support from Saha and funding from the Tatas, Nagchaudhuri had arranged for shipment of parts for a cyclotron magnet to the Calcutta University. However, ship carrying the second consignment of parts for the cyclotron was sunk by the Japanese. The team under the leadership of Saha and later under Nagchaudhuri took on the task of building the remaining parts themselves. Problems with the vacuum pumps continued to afflict the project. The demountable oscillators also proved difficult to build. It was only in 1954, after a visit from Emilio Segre to the laboratory, that the cyclotron started to function. Nagchaudhuri is thus credited with building the first cyclotron in India.