Police said about 20,000 people took part, while student organisers estimated the crowd at about 150,000.
The gathering in Santiago was largely peaceful, but violence broke out at the end when small bands of hooded protesters threw rocks and petrol bombs at police.
Authorities said seven police officers had minor injuries and 134 protesters were taken into custody.
Past student marches focused on pressuring President Michelle Bachelet to fulfil her campaign promise of education reform.
Students now say they are fed up waiting for changes and are disgusted by a series of corruption scandals involving politicians and the business elite.
The scandals include a controversy over a bank loan involving Ms Bachelet’s son and campaign financing involving right-wing politicians and a prominent financial company.
Another tax-related election-financing scandal at Chilean SQM mining company forced the resignation of its chief executive.
Aurora Isidora Rozas, a spokeswoman for the co-ordinating assembly of school students, said: “We need to protest against this caste of corrupt politicians and businessmen who are involved and who are not ruling for a majority.”
Students waved banners demanding changes to an education system characterised by poor state schools, expensive private universities and unprepared teachers.