"Our education will not pay your debt!" read a banner at the front of the march heading down one of Madrid's main avenues towards the education ministry, to the din of horns and whistles.
The national students' union that called the demonstration says Prime Minister Mariano Rajoy's conservative government has cut €5 billion ($6.5 billion) from public education budgets in the past year.
The government says the measures, part of major savings measures imposed last year, are needed to stabilize Spain's public finances.
"They are privatizing the universities and raising fees, cutting research and putting more students in each class," complained one demonstrator in Madrid, Jorge Barrio, a 20-year-old topography student.
"The only option I see is to go and work or study abroad."
The union said in a statement that university fees have been raised by up to two thirds and 80,000 teachers had been laid off.
A typical annual university fee has risen from around €1,000 to €1,500 — a relatively big hike in Spain's state-funded education system.
The recession in Spain has driven the unemployment rate among the under-25s above 50 percent.