Named after Johannisthal, which is named after its founder Johann Wilhelm Werner.
Johannisthal was founded under a contract of 16 November 1753 between Kammerrat (chamber councillor) Johann Wilhelm Werner and the Prussian state, during Frederick II’s settlement of the land, and is named after him. The station long served the S-Bahn workshops as Schöneweide Betriebsbahnhof and was renamed Berlin-Johannisthal in December 2020.