The alleged victim contacted police last November about assaults she said occurred in 2007 and again in 2008.
Police allege the teen was a regular passenger on the Calgary driver's bus when she was 14 and after some weeks he got her alone and sexually assaulted her.
Police say the two met up a year later and sexual contact began again.
Paul Rene Desmarais, 61, is charged with sexual assault, sexual interference with a child under 16 and sexual contact with a youth by a person in authority.
Police are asking anyone who has information to come forward.
City officials said the suspect is no longer working for the city, which is conducting its own investigation.
"We take this very seriously, and I have a genuine concern for everyone affected by this issue," city manager Jeff Fielding said in a news release Friday.
"How we perform our duties at work ... should be respectful, honest and based on a culture of integrity."
New transit operators are subject to police background checks before they are hired, he said. Screening includes police and security clearance, background and reference checks.