Paul Rene Desmarais, 61, has been charged with sexual assault, sexual interference with a child under 16 and sexual contact with a youth by a person in authority.
Police said Desmarais, who was 53 at the time, befriended a 14-year-old passenger in September 2007 and after several weeks, got her alone on his bus and sexually assaulted her.
"The teenage girl encountered the suspect again in March 2008 when she took another bus route," police said in a release.
The complainant told police Desmarais again assaulted her, this time at his home.
She reported the offences to police in November and on Feb. 12 Desmarais was arrested without incident, police said.
Desmarais is no longer employed by the city, officials said this week.
Anyone with information is asked to call the Calgary police non-emergency line at 403-266-1234 or contact Crime Stoppers.
Senior city officials, including Calgary Transit director Doug Morgan, are set to speak to the media about the allegations at 11 a.m. MT.