Witnesses say the armed man ran away after a busing the woman for about 30 minutes, and robbing other passengers.
The crime has shocked the country, becoming a topic of discussion on social media.
The rape of a tourist in late March had already raised concerns about security ahead of the football World Cup next year and the Olympics in 2016.
Days later, seven people died as a packed bus crashed off a bridge following an alleged argument between the driver and a passenger.
After these episodes, Rio de Janeiro's mayor, Eduardo Paes, vowed to tighten security and checks on public transport.
But Friday afternoon's attack comes as a fresh blow, correspondents say.
Witnesses told the authorities the assailant took a group of about 10 passengers to the front of the vehicle, telling the driver to keep on driving.
After taking their belongings, the man is said to have hit a 30-year-old woman with his gun before raping her.
The man, who witnesses said appeared to be under the influence of drugs, then got off the bus and ran across a busy motorway.
The crime has shocked the country, becoming a topic of discussion on social media.
The rape of a tourist in late March had already raised concerns about security ahead of the football World Cup next year and the Olympics in 2016.
Days later, seven people died as a packed bus crashed off a bridge following an alleged argument between the driver and a passenger.
After these episodes, Rio de Janeiro's mayor, Eduardo Paes, vowed to tighten security and checks on public transport.
But Friday afternoon's attack comes as a fresh blow, correspondents say.
Witnesses told the authorities the assailant took a group of about 10 passengers to the front of the vehicle, telling the driver to keep on driving.
After taking their belongings, the man is said to have hit a 30-year-old woman with his gun before raping her.
The man, who witnesses said appeared to be under the influence of drugs, then got off the bus and ran across a busy motorway.
