One of the organisers of the strike, Bela Breitner of School Strike Against Compulsory Military Service, said the federal government was "serious about gradually reintroducing compulsory military service."
At a protest in Hamburg, demonstrators waved flags and held up banners reading "We won't take part in your wars."
German Chancellor Friedrich Merz has made boosting Germany's military a priority following Russia's invasion of Ukraine. A new law introducing voluntary military service came into force in January, with the aim of recruiting volunteers to increase the number of soldiers.
However, if the security situation worsens or if too few volunteers come forward, a form of compulsory military service could be considered by Germany's Parliament, the Bundestag.
Under the law, all 18-year-olds in Germany are being sent a questionnaire asking if they are interested and willing to join the armed forces. The questionnaire is mandatory for men and voluntary for women, and all 18-year-old men will have to take a medical exam to assess their fitness for possible military service.
One protester, 16-year-old Elias Bernhard from Hamburg, said the responses to the questionnaires "show that young people do not want to join the Bundeswehr."
"That is why I am out on the streets today. That is why we are serious about striking until compulsory military service is off the table. We will carry on," he said.