Morris County Prosecutor Robert Bianchi said Comperchio allegedly parked his bus prior to making his normal rounds and assaulted the student on the bus.
Comperchio was identified as an employee of Byram Bus Lines, but authorities would not say what school the victim attended.
He is being held at the Morris County Correctional Facility on $100,000 bail.
A prosecutor's spokesman said he did not know if Comperchio had retained a lawyer.
Alan Mackerley, Jr. of Byram Bus Lines said the charges came as a shock.
"This is something that hit us out of the blue. My understanding is that this is under criminal investigation and we are cooperating with the authorities and the school board," he said.
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