Salah al-Din Al-Ayyubi (Saladin) assumed control of Egypt upon the death of the last Fatimid Khalif in 1171. When the Crusaders attacked Egypt, burning part of Cairo, Salah al-Din fortified the city and built the Citadel. His reign was a golden age for Egypt and Salah al-Din is revered as one of the greatest heroes of Islam, for his humility, personal courage, brilliant military and administrative mind and for defeating the Christian armies and treating the vanquished with dignity.

Salah al-Din spent eight years of his 24-year reign in Cairo, during which time he established the Seljuk institution of the madrassa, built hospitals and other infrastructure. Salah al-Din also introduced Mamlukes (an Arabic word meaning "owned"), Turkic slaves from the Black Sea region who had been raised as mercenary soldiers. Under Salah al-Din and his successors the Mamlukes were given a measure of freedom to own land and raise families and some rose to positions of power and influence.

Upon the death of Salah al-Din in 1193, he was succeeded by his brother, al-Adil, following a protracted succession dispute. Al-Adil died in Syria, upon hearing the news of the crusaders' seizure of the chain bridge (::I) at Damietta in 1218. He was succeeded by his son and Salah al-Din's nephew, al-Kamil, who drove back the Fifth Crusade. His successor, Sultan Ayyub, increased the size of his Mamluke army and married a slave girl called Shagarat Ad-Durr (Tree of Pearls). When Ayyub died, his wife became the first woman to rule Egypt since Cleopatra. She was the last ruler of the Ayyubids. Injunctions against women rulers placed Shagarat Ad-Durr in an untenable position and the Abbassids forced her to take a husband. When her new husband, Aybak, planned to take a second wife, Shagarat Ad-Durr had him murdered. She was assassinated shortly after this and the Mamluke military commander Baybars assumed control, ushering in the Mamluke period.