Caiden Mayor apparently fell asleep on his bus to Kemptville Public School on Thursday morning, and when the other children got off the bus, Caiden did not.
The apologetic driver found him hours later, alone in the locked vehicle and brought him home.
The Upper Canada District School Board has launched an investigation into the matter.
Caiden's father, John Mayor, says he was told the driver, who apologized profusely, offered to resign.
The Ontario Provincial Police have been called in to investigate.
"The bus driver told (my wife) that he didn't do his check when he parked the bus at his house, and that my son had been locked in the bus for a couple of hours," Mayor said.
"My son's eyes were puffy and red and he was crying and looked like he had been crying for a long time," he said.
Mayor said he wasn't contacted about Caiden not being in school despite protocols stipulating if there is an unexplained absence from school, administration must contact the child's parents.
School board chairman Greg Pietersma said such incidents are unacceptable and they will get to the bottom of the matter and find out why regular protocol was breached.