Following the disintegration of the Abbasid caliphate, control over Egypt fell in 936 CE into the hands of the Ikhshidis; shortly thereafter the Fatimids gained control over the country. The Fatimids, a branch of the Ismailis, were named after Fatima, the daughter of the Prophet. At the beginning of the tenth century the Fatimids established a kingdom in North Africa, which became a threat to Baghdad and to the Ikhshidis in Egypt. In 910 they appointed Immam Abidallah as caliph of the Muslim world, and set Qiron (Tunisia) as their capital. In 969, during the reign of the fourth caliph Al-Muiz, the Fatimids captured Egypt. Four years later, Al-Muiz established his new Fatimid Capital in Cairo (Arabic: the victorious; also the the planet Saturn – the time when the city was established). The Fatimids invaded Palestine in 970 CE, conquering it in 972. The Fatimid rule of Palestine was a time of great turmoil, and it is frequently referred to as the War of Sixty Years (969-1029 CE). Throughout this period, the Fatimids struggled against local Arab forces and Christians who were supported by the Byzantines and the Qarmatians. This period of unrest is echoed in the Cairo Geniza.

It seems that the Jewish population of Palestine supported the Arab rulers, perhaps aspiring to recapture the city through the Arab tribes. The Jewish settlement in Palestine flourished during the Fatimid period in Jerusalem, Ramla and Tiberias, albeit suffering too from the constant fighting. The stormy period of Fatimid rule affected the economic situation.The Arab Geographer, al-Muqaddasi, describes Jerusalem as a city in which life is difficult (985 CE).

The years immediately following the Sixty-Years War were a period of relative calm in Jerusalem, maintained until 5 December 1033, when a serious earthquake occurred, causing major damage to Ramla and Jerusalem, whose city walls and the walls surrounding Temple Mount were destroyed. caliph Al-Tahir engaged in restoration and construction works in Palestine, including the rebuilding of the city walls of Jerusalem, in which the Jewish population also participated. It seems that the restoration work was not completed, and twenty years later we hear that caliph Mustansir repaired the walls and towers of Jerusalem. The costs of these projects were imposed on the residents of Jerusalem. The end of the Fatimid rule in Palestine is related to the poor economical situation in Egypt, a result of an extended draught, and of the rise of a new force in the area – the Turcomans (Seljucs). In the summer of 1073 the Turcomans took Jerusalem for merely a short period of time until the summer of 1098. The Fatimids regained power for as much as a year, when the Crusaders captured the city in the summer of 1099.