After completing his doctorate in 1941, Nagchaudhuri returned to the Rajabazar Science College, University of Calcutta to join Saha's research group. In 1949, when the Saha Institute of Nuclear Physics (SINP) was established, Nagchaudhuri was affiliated with research at the institute, while continuing to teach at Science College, Calcutta University. After Saha's retirement in 1952, he was named Director of the SINP.