Joel Cedeno, 62, is charged with endangering the welfare of a child.
Police say he asked a 15-year-old girl, who was the sole passenger on his bus, to hug him last Tuesday morning.
When she offered to shake his hand, police say Cedeno kissed her.
The girl's mother reported the incident to Patchogue-Medford School District, which alerted the police.
Cedeno is due back in court on May 21.