The Citadel was fortified by the Ayyubid ruler Salah al-Din (Saladin) between 1176 and 1183 CE, to protect it from the Crusaders.

Only a few years after defeating the Fatimid Caliphate, Saladin set out to build a wall that would surround both Cairo and Fustat. Saladin is recorded as saying, "With a wall I will make the two [cities of Cairo and Fustat] into a unique whole, so that one army may defend them both; and I believe it is good to encircle them with a single wall from the bank of the Nile to the bank of the Nile." The Citadel would be the centerpiece of the wall. 

Built on a promontory beneath the Muqattam Hills, a setting that made it difficult to attack, the efficacy of the Citadel's location is further demonstrated by the fact that it remained the heart of Egyptian government until the 19th century.

The citadel stopped being the seat of government when Egypt's ruler, Khedive Ismail, moved to his newly built Abdin Palace in the Ismailiya neighborhood in the 1860s. While the Citadel was completed in 1183-1184, the wall Saladin had envisioned was still under construction in 1238, long after his death.