In 1971, when Pakistani army attacked in the University of Dhaka area, Choudhury escaped from there and moved to his parents' house, near Hatirpool. On 14 December 1971, he, along with a large number of Bengali intellectuals, educators, doctors and engineers, were kidnapped from their houses and later tortured and killed by the Pakistan Army and its Bengali collaborators Al-Badr and Al-Shams. According to a witness, Choudhury was last seen in Government Physical Education College, Dhaka in Mohammadpur Thana, Dhaka where his fingers were mutilated. His dead body was not found.