John Felix Clemons, 64, is charged with indecent liberties with a child and second-degree sexual exploitation of a child.
Bond was set at $80,000.
Police said the incident happened Tuesday on the bus Clemons drove.
The alleged victim is a student at Leesville Road High School.
A spokesperson for the Wake County Public School System said Clemons resigned from his job before his arrest.
He had been driving for the district since 2010.