The mosque of Al-Hakim was built in 990. Its construction began under Al-Aziz Billah, the father of Al-Hakim bi-Amr Allah, but the mosque was finished and completed under Al-Hakim in 1013 so it was named after him.

The mosque is considered one of the main religious sites in Egypt, due to its architecture, despite not being a very large mosque. The trademark that makes this mosque unique is its beautiful minarets. The minarets of this mosque are unique and different to the other mosques in Egypt. The mosque’s minarets have a square base which they are beautifully elongated from their centres. They are cylindrical in shape, hollow from the inside and on the top they are finished in a “Mabkhara” shape. The minarets also have mihrab shaped carvings into them. The mosque is also known for its richness in Kufi inscriptions, which some are preserved and survived till today, while some didn’t. The original mosque was said to have twelve thousand feet of inscriptions.

After the Fatimids, the mosque was used as a prison for the captured crusaders, as a stable by Saladin and as a fortress by Napoleon, as well as a warehouse by the surrounding shops in later years. The mosque slowly fell out of its original image and was in a very bad condition. In 1980, the mosque was restored by Mohammed Burhanuddin, the leader of the Dawoodi Bohras, a Shia sect. The Bohras asked president Anwar El-Sadat to allow them to restore the mosque and he accepted, and was invited to the opening of the mosque after it was finished.