Police in Dunmore, near Scranton, found the boy in the car with the Rev. W. Jeffrey Paulish Thursday at the Penn State University Worthington Scranton campus.
An arrest report said officers were investigating a report of a suspicious vehicle when they found Paulish and the boy. Paulish allegedly told officers the youth was troubled and he was providing counseling.
Paulish was charged with three misdemeanor counts of indecent contact with a person under 16, indecent exposure and corruption of a minor.
Paulish later told officers he had arranged to meet with the boy through Craigslist, The (Wilkes-Barre, Pa.) Times-Leader said.
CNN said the Scranton diocese issued a written statement urging anyone else who may have been sexually involved with Paulish to contact Lackawanna County prosecutors.
Paulish was being held on $50,000 bail.