The S3 departs from Erkner through the woods and on the lakeside of Köpenick. It travels through the heart of Berlin with stops at Friedrichstraße, Berlin Hauptbahnhof, and Olympiastadion with a final stop in Spandau. The line runs every 20 minutes.
From Monday to Friday, the line runs at 10-minute intervals between Erkner and Charlottenburg during peak times. Outside peak times, the line runs at 10-minute intervals only between Friedrichshagen and Ostbahnhof. During the summer, the S3 runs every 10 minutes between Erkner and Ostbahnhof on Saturdays and Sundays; but in the winter, there is only a 10-minute interval between Friedrichshagen and Ostbahnhof on Saturdays and Sundays.
Together with the S9, the S3 runs between Ostbahnhof and Spandau at 10-minute intervals. Additional trains will operate between Karlshorst <> Ostbahnhof from Monday to Friday at 20-minute intervals (These trains are not available during the Christmas and summer holidays.). The S3 runs every 30 minutes through the night on Friday and Saturday between Erkner and Ostbahnhof.