Egyptian forces fired tear gas at students on Tuesday before taking control of all buildings and dormitories in Cairo’s Nasr City.
A spokesperson for the Azhar Student Union said dozens, including female students, were arrested in the raid.
Tensions continue to run high in Egypt, which plunged into deadly unrest since the country’s first democratically-elected president, Mohamed Morsi, was ousted by the army in early July.
The military also dissolved the parliament, suspended the constitution, and appointed head the Supreme Constitutional Court, Adly Mahmoud Mansour, as the country's interim president.
Egypt is now bracing for more violence ahead of an upcoming referendum on a new constitution drafted after Morsi’s ouster.
Supporters of Morsi argue that the amendments made to the 2012 charter are against all constitutional articles related to the country’s Islamic identity and values.
The Muslim Brotherhood, which has been leading protests demanding the reinstatement of Morsi, has already said that it will boycott the “illegitimate” vote.
The group also says that the constitution runs contrary to the objectives of the 2011 revolution that ended decades of rule by former dictator, Hosni Mubarak.
The new constitution, drafted by a 50-member committee on December 1, bans religion-based political parties.
It also consolidates the power of the army, which under the new charter can prosecute civilians in military courts, appoint the defense minister, and keep its budget beyond any civilian scrutiny.