In 1958, Alam joined the Pakistan Atomic Energy Commission as a researcher, and was directed to join the Institute of Nuclear Science and Technology (PINSTECH), the national laboratory site in Nilore, in 1970. During the war with India in 1971, Alam became interested in computing and mathematics, briefly writing a computer program while working in problems relating to logic and the mathematics. Alam was instrumental in establishing the computer department at the Institute of Nuclear Science and Technology before moving to join the Physics Division.