The victim, who has the mental capacity of a 10-year-old, did not scream for help, but she told the driver she had been raped after the assailant exited the bus, Scott said.
Trotter, who is unemployed, has previous convictions for grand theft and possession of rock cocaine, according to court records. He was previously investigated for sexual assault, but no charges were ever filed, Scott said.
Trotter and his victim do not know one another. Authorities wouldn't say if DNA evidence had been recovered.
"We believe it was a crime of opportunity, that unfortunately she was in the wrong place at the wrong time," Scott said.
It was the third rape so far this year on county buses that annually carry millions of people.
Bus drivers are trained to call transit dispatchers when they become aware of a possible crime, said Marc Littman, a spokesman for the Metropolitan Transportation Authority. If a crime is in progress, there is a silent alarm on board that can be tripped.
"This is an extremely rare occurrence," he said.
It was unclear if the driver saw what transpired. He was being interviewed by authorities.
"We don't believe anybody else did anything wrong," Scott said.