The incident took place in the southeastern neighbourhood of Friedrichshagen on Tuesday, according to the police report.
But the driver announced over the loudspeaker that she should get out of the vehicle, saying he would not drive anyone who wears a headscarf, the girl told police.
According to her account, she did not receive support from any of the other passengers and left the vehicle, unsure of what the right thing to do was.
She later discussed the incident with an adult, who then reported it to authorities.
The Berlin Transport Company (BVG), which promotes itself as young, hip and liberal, told Tagesspiegel it was looking into the incident.
Examination of the relevant CCTV footage would last until Thursday, the company said.
BVG released a wildly popular video last year listing all the things people can get away with on its trains, trams and buses - the message being that as long as Berliners pay their fares the BVG lets them follow any lifestyle they want.
In a separate incident, a 17-year-old reported being attacked in the Prenzlauer Berg neighbourhood in the northeast of the city by four men who had showed him the Hitler salute, Die Welt reports.