The first rape allegedly took place in November 2011 in a park in the Lichtenberg area of east Berlin.
The girl, aged 15, was supposed to meet one of the boys, then aged 16, but he brought three of his friends with him, aged 13, 14 and 16 at the time, where they attacked her near a church, the Bild newspaper reported.
According to the state prosecutor she was then raped on a park bench.
She did not tell her parents and eight months later was allegedly raped by the same four boys again in a basement. It was only then that she went to the police with her parents.
The case will now be heard by a youth court.