The interior of the mosque is divided into a courtyard and an arcade of keel-shaped arches, with the south-east (qibla) side of the mosque extending deeper to create a prayer hall three rows deep. The mosque’s original design did not include the arcade on the northwest side (the side with the main entrance), which was inadvertently built during the Comité restoration in the 20th century. The inside is decorated with stucco-carved window grilles, wooden tie-beams between columns, and Kufic-style Qur’anic inscriptions on the outlines of the prayer hall’s arches. The extant Kufic inscriptions in the prayer hall show a very elaborate late-Fatimid style in which the letters are carved against a background of vegetable arabesques, but much of the inscriptions around the arches have already vanished.

The mosque was erected on an elevated platform with built-in alcoves on three sides (all save the qibla side) that were intended to house businesses that supported the mosque financially. Thus, it was Cairo’s first “hanging” mosque—that is, a mosque with a prayer area that is elevated above street level. A main entrance to the northwest and two lateral entrances on the sides make up the mosque’s three entrances. The front (north-western) entrance is flanked by a portico with five arches, a feature that was unusual in Cairo (at least before the much later Ottoman period). If the head of Husayn had been buried here as intended, the portico may have served as a royal viewing platform for processions through Bab Zuweila or for some other ceremonial purpose. One of only a few Fatimid-era ceilings of its kind that have been preserved is the original ceiling just beneath or inside the portico. The wooden doors at the mosque’s entrance today are reproductions of the originals, which are now housed in the Museum of Islamic Art, as was previously mentioned. Over the mosque’s entrance there used to be a minaret, but it was damaged in the 1303 earthquake. A subsequent minaret built during the Ottoman era was eventually taken down during restoration work in the 20th century. Its old location is most likely indicated by the stairs that is still visible and connects to the roof today.