The Fatimids Khalifa Al-Aziz Billah began the construction of this mosque in 380H (990). His son Al- Hakim Billah, the third Fatimids Khalifa of Egypt, completed it in 403H (1013); the mosque being named after him. This, the second Fatimids mosque in Cairo, was situated outside the old walls of the city, until Badr Al-Gamali brought it within by constructing the north wall (extending from Bab AL-Nasir to Bab Al-Futuh) , in contact with its northern façade. In the year 702H. (1302-1303), as a result of an earthquake, the tops of the two minarets of the mosque collapsed, and the whole structure cracked.

Courtyard and ground plan of Al-Hakim Mosque in Cairo where it stood outside the old city wall before Al-Gamali had the fortifications renovated. The five-aisled prayer hall has a wide raised central aisle. The old courtyard, which was allowed to fall into dilapidation and is largely destroyed, was sometimes used as a military barracks in the past, and later as a sports ground.
 

In 703H (1304), Baybars Al-Gashankir, by order of Al-Nasir Muhammad ibn Qala'un, restored the two minarets and the fallen arches. Traces of this restoration can still be observed in the present tops of the two minarets and in some of the sanctuary arches, which differ from the original ones for they are of horse- shoe form, while the others are pointed. Evidence of this restoration can also be noticed in the pierced stucco windows in the drum of the dome over the mihrab, and in an historical inscription over the main entrance, recording this restoration and dated 703H (1304). Ever since that event, history does not record any serious restorations having been executed in this mosque. What remains of it, however, enables us to realize its original dignity and majesty. Many original parts of the sanctuary have been preserved such as the transept with its arches and piers, the dome over the mihrab and some arches to right and left of the transept. Parts of the decoration, which have survived all those centuries, can still be seen in the bands of Kufic, executed in stucco, below the ceiling and the square base of the dome, as well as in the stucco windows, pierced with beautiful ornaments and Kufic inscriptions with geometrical designs penetrating them. Original also are the carved wooden tie- beams of the arches under the dome.

It is possible to reconstruct the mosque in its original form with the aid of the parts still standing. It bears a great resemblance to mosques which preceded it, for it has an open Court surrounded by four covered hallways. The sanctuary is five aisles deep; its arches are supported by rectangular piers with engaged brick columns at the corners. Each of the two lateral hallways is three aisles deep while the back one is two only. A transept runs through the middle of the sanctuary, from the Court to the mihrab. At the two back corners of the sanctuary were two domes; the drum of the southern one has been restored while nothing but a small part of the other remains. Of the original mihrab, nothing remains except the recess. The marble lining which was prepared under the auspices of Al-Saiyid 'Umar Makram in 1223H. (1808-1809), when part of the sanctuary was used as a corner for prayers, was transferred by the Department for the Preservation of Arab Monuments as a lining to another mihrab which the Department has made in the Qibla wall, to the right of the original one. The Department has, in the meantime, pulled down the stone doorway of this corner and rebuilt it in the Court.
 

The Mosque of Al-Hakim measures nearly 120 x 113 Meter and has several entrances besides the main one in the middle of the west façade; the most important of these are two to the left and two to the right of main entrance and one in the centre of the north and south façades. The ziyada which it once had, next to its south façade, is now occupied by later buildings. As regards building material, this mosque bears a great resemblance to the Mosque of Ibn Tulun. Brick was used in both mosques, except that the outer walls of al- Hakim's are built of partly dressed stone (talatat). This similarity may be observed in the shape of the piers which support the arches, and in the style of the Kufic inscriptions of the frieze below the ceiling, which however are carved on wood, whereas in the Mosque of Al-Hakim, they are carved on stucco.
 

As regards the transept which divides the sanctuary, and the dome in front of the mihrab, we can find a similar arrangement in al- Azhar mosque. The two domes at the back corners of the sanctuary again recall those which once existed in al- Azhar. An architectural feature which distinguishes the west façade, is the stone salient which projects centrally from it, forming the monumental entrance of the mosque. We have not come across such a feature, prior to this, except in the Mosque of Al-Mahdiya which was built at the beginning of the fourth cent. H. (beginning of tenth cent. A.D.), and later on in the mosque of Al-Zahir Baybars Al-Bunduqdari. At the north and south ends of this façade, stand two salient towers, each formed of two hollow cubes, one above the other. The lower cubes are of the same period as the mosque while the upper are work of Baybars Al-Gashankir.