He was born into the Mirghani family in Mecca which was one of the most noble families that have descended from the Islamic prophet Muhammad. He is the son of Muhammad Abu Bakr who is the son of AbdAllah al-Mahjoub who is the son of Ibrahim who is a descendant of the Prophet Muhammad. The lineage of Muhammad Othman al-Mirghani was verified by Murtada al-Zubeidi and this was further verified by al-Jabarti in his book "Taareekh al-Jabarti / al-Jabarti's History" part two.