When the train ended up at the last stop, the Coney Island Stillwell Avenue station in Brooklyn, police she was approached by a man who apparently thought she was a prostitute.
He reportedly asked her for her rates, she declined to talk to him and he walked away.
The victim then fell asleep, authorities say, and when she woke up at the next stop, she found the same man clutching a boxcutter.
She claims the man threw her to the ground and raped her on the subway floor.
He got off at the next stop, and she ran to get the train conductor. She was taken to Coney Island Hospital for treatment.