Siddiqui was a founder-member of the Indian and Pakistan Academies of Sciences, and later a founder member of the international body the Third World Academy of Sciences. The following are the honours he received, in reverse chronological order:
* Gold medal of the Soviet Academy of Sciences
* Third World Academy of Sciences – TWAS Prize, 1985
* Hilal-e-Imtiaz, (Crescent of Excellence) 1980 by the Government of Pakistan
* President of Pakistan's Pride of Performance Medal, 1966
* Sitara-e-Imtiaz, 1962 (Star of Excellence) by the Government of Pakistan
* Fellow of the Royal Society, 1961
* President, Pan-Indian Ocean Science Association, 1960
* Tamgha-e-Pakistan, 1958 (Medal of Pakistan)
* D. Med. Honoris causa from the Frankfurt University, 1958
* Foundation Fellow, Pakistan Academy of Sciences, 1953
* Order of the British Empire in 1946