Security forces and pro-regime gunmen from the Shabiha militia stormed a student dormitory, firing tear gas and live ammunition to disperse the 1,500 students living there, according to student activist Thaer al-Ahmed.
The violent confrontation left parts of the campus on fire.
Others suffered cuts and broken bones as they tried to flee.
The agency reported the protesters had also been attacked by students loyal to President Bashar al-Assad prior to the security forces' raid.
The raids lasted for five hours, with one eyewitness reporting that students were thrown off the roofs of dormitory buildings.
Aleppo has remained mostly loyal to the Assad regime, escaping the violence and destruction seen in other parts of the country over the past 13-months.
But students in the city have been staging almost daily protests.
The latest reports of violence come only a day after fighting in Syria escalated, with troops loyal to al-Assad suffering their worst loss of life since the start of the failed United Nations-mandated cease-fire three weeks ago.
Rebel forces reportedly killed 20 troops in a series of pre-dawn raids, including two colonels and 15 soldiers during an attack in Aleppo, according to the Syrian Observatory for Human rights.
The latest clashes come as activist group Human Rights Watch (HRW) accused the Syrian army of committing war crimes in a new report documenting the killing of at least 95 civilians in Idlib province two weeks before the start of the April ceasefire.
In its 38 page report, They Burned My Heart: War Crimes in Northern Idlib during Peace Plan Negotiations, HRW claimed that government troops carried out, dozens of extrajudicial executions, killings of civilians, and destruction of civilian property that qualify as war crimes, as well as arbitrary detention and torture.