The president of Al-Azhar University, Osama El-Abd, has been sacked after hundreds of students suffered food poisoning on Monday.
Al-Azhar’s supreme council has called for elections to be held within two weeks to select his replacement.
Previous presidents, including El-Abd, were appointed by the head of state.
El-Abd was appointed by the Supreme Council of the Armed Forces in 2011.
Around 500 students were hospitalised on Monday after eating at a cafeteria on the Al-Azhar campus.
Thousands of students marched on Wednesday afternoon from the campus in Nasr City to Al-Azhar Sheikhdom in Cairo's Darrasa district. They chanted against the university's president and management.
Shortly after the food poisoning came to light on Monday, hundreds of angry students gathered at the university's dormitory building.
On Tuesday, hundreds of students broke into the university headquarters in Nasr City and some of them called for the resignation of El-Abd.
President Mohamed Morsi visited some of the ill students in hospital on Tuesday morning.
The last of the students were discharged from hospital on Wednesday, an official at Al-Azhar said.