Sen Gupta was born on 1 August 1934 in Barisal in the then Bengal Presidency of British India to Suruchi Bala and Jitendra Nath Sen Gupta. He obtained his Ph.D. in nuclear physics from the University of London in 1963, under the supervision of Joseph Rotblat. His doctoral thesis studied the scattering of Helium-3 particles. He stayed back in the United Kingdom conducting his postdoctoral research at the Nuclear Physics Laboratory at the University of Oxford between 1973 and 1976, and at the Department of Physics, University of Birmingham between 1981 and 1982.