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.
In recognition of his scientific leadership, Frankfurt University granted him the degree of D.Med. Honoris causa in 1958. Also in 1958, the Government of Pakistan awarded him with Tamgha-e-Pakistan. In 1960, he became the President of Pan-Indian Ocean Science Association. The same year, he was elected Fellow of the Royal Society. In 1962, he was awarded the Sitara-e-Imtiaz for distinguished merit in the fields of science and medicine. Siddiqui remained the director and chairman of PCSIR until the time of his retirement in 1966. In that year, the President of Pakistan awarded him the Pride of Performance Medal for the respectable completion of his service.
In 1967, Siddiqui was invited by University of Karachi to set up a Postgraduate Institute of Chemistry in affiliation with the Department of Chemistry. He was designated as the institute's Founder Director, whereas the additional research staff was provided by PCSIR.
In 1976, the institute was offered a generous donation from Hussain Jamal Foundation. In appreciation of this donation, the institute was renamed as Hussain Ebrahim Jamal Research Institute of Chemistry. In due time, Siddiqui transformed the institute into a distinguished centre of international excellence in the field of chemistry and natural products. In March 1975, he headed the National Commission for Indigenous Medicines His tireless efforts for the promotion of science and technology earned him Hilal-e-Imtiaz by the Government of Pakistan in 1980. In 1983, he played a major role in the establishment of the Third World Academy of Sciences and became its Founding Fellow. He remained the director of the Hussain Ebrahim Jamal Research Institute of Chemistry until 1990. Later on, he continued research in his personal laboratory. He published over 400 research papers and was granted 50 patents.