For most of its existence since becoming a numbered route in 1984, the S3's line colour is blue.

[2] S3 originally was shortened to Ostbahnhof from 2003 to 2009 while awaiting renovation works.

To compensate for the diminished throughput on the Stadtbahn, the S3 (formerly Erkner ↔ Ostbahnhof) was extended westwards to Spandau.

The S3 was created along with the S1 and S2 on 9 January 1984, when the Berliner Verkehrsbetriebe (BVG) took over the S-Bahn network from the East German Deutsche Reichsbahn (DR) in West Berlin: the S3 initially ran between Friedrichstraße and Charlottenburg, before being extended south-westwards to Wannsee on 1 May 1984.

[3] Due to the reunification of Germany, the S3 briefly became a four-coloured line on 1 July 1990, absorbing the DR S-Bahn services formerly terminating at Friedrichstraße to Strausberg Nord (orange), Erkner (yellow), Königs Wusterhausen (green), and Flughafen Berlin Schönefeld (sky blue, now BER Airport – Terminal 5).