According to El Maqrizi, the renowned historian, after he died in the tragic battle of Karbala in 61 AH (680), his head was moved from Ashkelon in Palestine to Cairo in 548 AH (1153 AD), where it rested in The Emerald Palace. Then, it was moved to its current dome, which was custom-made for the head in 549 AH (1154 AD), where it has remained since then, lying three stories down.

According to Souad Maher Mohamed's 2017 book Egypt's Mosques and Its Pious Wallies, during Saladin Al-Ayubi’s reign, a religious school and hostel for religious fiqh teachers were built outside the dome in 578 AH (1184 AD). Sadly, a big fire destroyed the joined building in 640 AH, and the place was renovated and turned into a mosque.

Since then and throughout the different eras, Ayubids, Fatimids, and Othmans until a couple of years ago, the mosque connected to the dome has been rebuilt and renovated.

The ancient dome is said to cover a silver coffin, where the head is neatly settled, and that a special room joined to the dome beholds some of the belongings of Prophet Muhammad, such as his Kuhl bottle, one of his shirts, and handwritten copies of Quran by each of Al Imam Ali Ibn Abi Taleb and Othman Ibn Affan were on display among other items.

Al-Hussein was beheaded in the most tragic battle in Islamic History which occurred between the party of Al-Hussein Ibn Ali, grandson of the prophet Muhammed and Yazid Ibn Umayya.

Since the head was buried in the district carrying his name, El-Hussein Mosque and Museum became a tremendous religious site in Cairo. People would flock from all over Egypt to pay a visit and recite El Fatha to the grandson of Prophet Muhammad. Moulid of Al Hussein is known to be one of the biggest events on the Sufi calendar and is celebrated on 25 Rabia Al Thani.