He succeeded his father Abu Mansur Nizar al-Aziz in 996. He continued the building of a mosque in Cairo begun by his father, completing it in 1013 (the Al-Hakim Mosque).

In 1009 he destroyed the Church of the Holy Sepulchre in Jerusalem, then under Fatimid control, and persecuted the Christians and other dhimmis in Palestine. Although the Church was rebuilt by Byzantine emperor Constantine IX in 1048, its destruction was remembered by Christians in western Europe for the rest of the century. Despite the relatively good conditions in the Holy Land under al-Hakim's successors in the 11th century, the destruction of the Church was used to support the First Crusade; in 1096, after the Council of Clermont, there was even a forged letter published, supposedly written by Pope Sergius IV, calling for a Crusade in 1009.