The mosque was built by Ibn Tulun in 879 AD on Mount Yashkur in a settlement named al-Qata'a, about two kilometers from the old community of Fustat. Ibn Tulun was born in Baghdad, the son of a Turkish slave owned by the Caliph al-Ma'mun, and became governor of Egypt.

Ibn Tulun Mosque was the third congregational mosque to be built in what is now greater Cairo. It has an area of about 26,318 square meters, which makes it the third largest mosque in the world. It is the oldest mosque in Egypt that has survived in a fairly original form. It was built over a period of three years, entirely of red brick. This is covered with a layer of stucco, carved with geometric and floral motifs inspired by the mosque in Samarra

When the city center moved away from al-Qata'a and to present day Cairo, the mosque fell into disuse. In the12th century it was damaged when used as a shelter for pilgrims from North Africa to the Hijaz, but restored in 1296. It was also restored in later periods with the latest restoration in 1999.

The mosque is surrounded by an enclosure called a riwaq, the widest being on the qibla side. Surrounding the mosque on three sides (all but the qibla side) are narrow enclosed wings called ziyadas, and the mosque's famous minaret with its external spiral ramp is located within the northern ziyada. The extensions bring the mosque as a whole almost to an exact square shape which ensure quiet and privacy for worshippers. Both the enclosure walls and the walls of the ziyada are surmounted by crenellations, a fortified parapet with alternate solid parts and openings, probably also of Samarra influence.
The on;y spiral stone minaret in Cairo has a mabkhara finial, the ribbed helmet carried on an open octagonal structure which was built in 1296.

The ablution fountain and dome were built on the site of a decorative fountain built by Ibn Tulun and destroyed by fire in 986. The fountain was set in a pavilion topped by a dome carried on gilded marble columns. The dome today is less ornate.

Since its renovation in 1999, the courtyard has been paved and the fountain refaced in black marble. The original design in the stucco in the pillars and around the 300 windows is being restored to its original state as are the crenellations around the walls.