Siddiqui migrated to Pakistan in 1951, four years after the emergence of Pakistan in 1947, after being offered and appointed as "science advisor" to the government by Prime minister Liaquat Ali Khan. He was appointed as Director of the Pakistan Department of Research that was reformulated in 1953 as Pakistan Council of Scientific and Industrial Research (PCSIR). The aim of PCSIR was to support the industrial infrastructure through research and development. The regional laboratories of the institution were located in Dhaka, Rajshahi and Chittagong (East Pakistan), and in Lahore and Peshawar (West Pakistan). In 1953, he founded the Pakistan Academy of Sciences as a non-political think tank of distinguished scientists in the country. In 1956, when Government of Pakistan established Pakistan Atomic Energy Commission (PAEC) as an atomic research agency, Siddiqui was designated as its technical member.