They joined students in over 2,000 cities across the globe as part of the global movement "Fridays for the future."
"There is no planet B" and "What I stand for is what I stand on" were just some of the messages written on placards carried by the demonstrators.
"Those who do nothing have no right to complain, and we have a lot of things to complain about and that's why we are here," a student called Erika said, while her colleague Igor was filming the whole event to show it in his YouTube vlog.
"I think we will manage to change something. There are a lot of us and I think this will help in stopping climate change, at least to a small extent," Igor said.
During their march from Europe Square to St Mark's Square, the seat of the government, the demonstrators stopped tram traffic in the main square Trg Bana Jelacica.
"We are here to show our resistance to the system that acts as if climate change does not exist. As a member of the European Union, Croatia is among developed countries and should treat the problem of climate change seriously," one student, Ana Zerjav said.
Another student, Laura Skala, who launched the Facebook page "School Strike 4 Climate Croatia" and initiated today's protest, in her address asked politicians what have they done to stop climate change. "Have you banned single-use plastic, have you made any investments in solar and wind energy? You haven't!"
She recalled that people had 11 years left to reduce greenhouse gas emissions by 50 percent to stop further temperature increases globally.
Skala told Hina she had coordinated the protest with students from other Zagreb schools and was pleased with the support of students and school heads.
Similar protests were also held in several cities across the country, including Split, Osijek, Krizevci, Varazdin, Pula and on the southern island of Vis.
The protests were supported by the Ministry of Environment and Energy, Minister of Science and Education Blazenka Divjak, and Croatian scientists.
Protests in European cities were inspired by 15-year-old Swedish student Greta Thunberg, whose strike for climate held outside the Swedish parliament in Stockholm every Friday since August 2018 has triggered the global movement "Fridays for the future."