It was the third rape so far this year on county buses that annually carry millions of people.
"This is an extremely rare occurrence," said Marc Littman, a spokesman for the Metropolitan Transportation Authority.
Trotter was booked for investigation of rape and was being held on $1 million bail, authorities said. It wasn't immediately known if he had retained an attorney.
He has previous convictions for grand theft and possession of a controlled substance, according to online court records.
Sheriff's investigators said they received an anonymous tip that led to Trotter's arrest after an image of the suspected attacker taken by a surveillance camera on the bus was publicly released.
The attack lasted about 10 minutes before the man stopped and exited the bus, authorities said. After the assault, the woman, who has the mental capacity of a 10-year-old, reported it to the driver who notified authorities, sheriff's Sgt. Dan Scott said.
Authorities have not yet located the person who witnessed the rape. Scott would not say if investigators found DNA evidence.
Bus drivers are trained to call transit dispatchers when they become aware of a possible crime, Littman said. If a crime is in progress, there is a silent alarm on board that can be tripped.
It was unclear if the driver saw what transpired. He was being interviewed by authorities.
"We want to see if protocol was followed as well," Littman said.