The fact checker in question is Correctiv, a German non-profit body of investigative journalists.
It will still be possible to share posts from fake news websites, however a warning will display that the veracity of the site is disputed.
Facebook is also testing the system with fact-checkers in the United States, who must sign up to Poynter's code of principles, of which there are currently 43 signatories internationally, including several news organisations.
Last week, BuzzFeed found that Facebook pages with large followings were publishing fabricated stories about Chancellor Angela Merkel who is currently seeking re-election.
German Justice Minister Heiko Maas has repeatedly called on Facebook to respect the country's defamation laws and monitor fake news on the platform.
In October last year he complained of an 'all talk' approach by the social network:
In spite of all the announcements by Facebook, our prosecutors are still compelled to fill hours of meaningless forms, which stay unprocessed by Facebook.