The rally in Germany's northern port city was led by Swedish teen activist Greta Thunberg, who has become a prominent voice in campaigns against climate change.
In January, the 16-year-old spoke at the World Economic Forum in Davos, Switzerland, telling business and government leaders: "I want you to panic. I want you to feel the fear I feel every day."
At the Hamburg protest, students held banners featuring slogans such as "March now or swim later" — a reference to rising sea levels from melting ice caps — and "We (heart) Greta."
Speakers at the rally also took aim at Germany's plan to phase out the use of coal by 2038, a timeline they consider too slow to curb emissions of carbon dioxide that are heating the atmosphere, AP reported.
Similar protests were planned in dozens of European cities and further afield.
There have been mixed reactions to the protests from German authorities, with some criticizing the fact that students are missing lessons to take part.
"Nobody is going to make the world a better place by skipping school," Hamburg's top education official, Ties Rabe, said on Twitter.
Thunberg suggested that it is in politicians' hands to end the protests, by taking tougher measures to prevent potentially catastrophic climate change.
"We will continue to school strike until they do something," she said. "We are striking because we have done our homework and they have not."