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.