Police used tear gas and water cannons against protesters in the city centre, which was strewn with debris and vandalised bicycles and street signs.
Some windows had been smashed.
Brussels police advised people to avoid the area around the city's main railway station.
Belgian media also reported protests in other French-speaking cities, including Namur and Charleroi, although they were mostly calmer than those in Brussels.
Belgium's French Community government, which oversees French-language education, plans to increase annual tuition fees for higher education to 1194 euro ($A1950) from 835 euro for the majority of students.
Although still low by international standards, it represents a 35 per cent increase - which the government says is part of a cost-cutting drive and brings fees broadly into line with those in Flemish, Dutch-speaking universities.
Other proposed measures include requiring teachers with pupils in the final years of secondary school to take on two extra classroom hours per week without additional pay, and revising tenure rules.
"We will have to work more for the same wages, and working conditions will deteriorate, with more people having larger classes," one teacher attending the protest who gave her name only as Marie told Belgian broadcaster VRTNWS.
At a press briefing on Thursday, French Community government leader Elisabeth Degryse defended the fee increase in the face of strained public finances, adding that the government was heading for a 1.9 billion euro deficit.
"Our aim with these measures is to free up money to re-invest in the sector", Education Minister Valerie Glatigny said.
The parliament of the French Community is expected to vote on the proposed cost-cutting measures later on Thursday.
9°C