They marched from outlying districts before merging in a planned protest outside city hall. The rally was timed to coincide with the announcement of the latest budget cuts by the Berlin government.
This year's school, youth and sport budget is to remain at around the same level as last year's, thus signalling no improvement in alleviating the critical cuts already implemented on the Berlin education system.
A shortage of books and teachers is a common scenario, with classes too full and schools in urgent need of renovation.
The marching pupils carried placards carrying messages like "Make cuts to the big shots not to school pupils", and "You are cutting off our future".
Nicole, 15, said of the standard of toilets in her school: "What I would give to be able to go to the toilet without having to feel totally sick. Sometimes I have to go."
Her fellow pupil, Nancy, 14, added: "There are holders in there for paper and soap but there is never anything in them."
Many main city centre roads were blocked off until early evening to allow the pupils to demonstrate.
There was only one minor, brief incident, when pupils threw eggs at a fountain statue near city hall.
Other students appealed to the small group to stop, using megaphones and saying: "We are allowed to gather here. We want to leave the square in the same condition as we found it."
The demonstration was supported by the Union of Education and Science (GEW). Speeches were held at the closing rally in front of the Brandenburg Gate, where the protesters marched, after lodging their complaints with city hall.
Berlin city government currently has debts of more than 5.45 billion DM (Pounds 2.02bn) and is continuously taking out credit to make ends meet. In 1995 the city borrowed 2.2 billion DM. The final figure for last year is expected to be more than 4 billion DM. The city has been on the verge of bankruptcy for more than a year.
Work and professional training, affecting many school-leavers, will face cuts this year, despite record youth unemployment in the city.
Only a few teachers took part in the demonstration. One, from an inner-city school said: "The cuts affect lessons in many ways more than the few hours teaching time lost because of the demonstration."