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It is located at Al-Mo'ez Ledeen Ellah Al-Fatimi Street next to the Bones Well which belonged to one of the old monasteries. The Mosque  was built by Vizier Abu AbdEllah Mohammad Al-Bata'ihi titled Al-Ma'moun,during the reign of the Caliph Al-AmerBeahkamEllah in 519 H\ 1125 AD. During the CircassiansMameluke Era,El AmirYalbogha Al-Salemi renewed the mosque because he took many positions at the reign of Sultan Barquqe, speciallythose related to convents as he was a mystic (Sufi).El Amir was prisoned in Alexandria then he was strangled in his prison while he was fasting during the reign of Sultan Al-NaserFarag Ibn Barquqe.

In 799 H., Yalbogha Al-Salemi renewed the Mosque's minaret, pulpit and the animal basin next to it.Hebuilt a hanging water pool in the court, stores, residential floors the highest one at the Mosque's northern door and he registered all these achievements on a marble tablet on top of the prayer niche (Mihrab).

In 815 H., the minaret was removed because of a lean in its construction. The mosque consists of a middle courtyard surrounded by four shelters the sanctuary is the largest, the ceiling of the mosque is of shallow domes, the arches of the courtyard has stucco decorations and verses from "surat Al-Nour", whereas the façade of the mosque is of stone, it has recesses of ribbedarches and Shiasentences the most important is the circle with the same center and at the middle the two words "Mohammad and Ali" are written, the northern edge is beveled because it has a side lane and ends at the top with  niches.At the beginning of the 20th Cen. AD, the façade of the Coptic Museum was designed on the same style of the façade of Al-Aqmar Mosque, with added crosses and Christian sentences instead of the Islamic ones as a sign of the unity between Muslims and Christians in Egypt.