The Nigeria Supreme Council for Islamic Affairs (NSCIA) was established in 1973 at a national conference of Nigerian Muslim leaders in Kaduna under the auspices of Jama'atu Nasril Islam (JNI), the group for all the Islamic organisations in Northern Nigeria. In the South-West, prior to this conference, the first Muslim organisation to be formed after independence in 1960 was the United Muslim Council (UMC), but this was embraced by few Muslims in the Western Zone as it was championed by the ruling political party. According to Adegbite, the emergence and coming together of the Western Joint Muslim Organisation (WESJOMO), the Najah Joint Muslim Organisation (NAJOMO) and the Nigerian Muslim Council (NMC) of Lagos State enabled the region to work hand-in-hand with the JNI to create in 1973 the Nigerian Supreme Council for Islamic Affairs.

Muhammadu Sa'ad Abubakar, CFR is the 20th Sultan of Sokoto. As Sultan of Sokoto, he is considered the spiritual leader of Nigeria's Muslims.