The 8-year-old girl was in the hospital on Friday after someone on the street threw a rock the size of a baseball into the bus.
The bus was transporting students from a local Jewish day school Wednesday in the northbound lanes of the New Jersey Turnpike in Teaneck Township just after 2 p.m.
The bus was heading back to Yeshivat Noam from a field trip to the Liberty Science Center in Jersey City when it happened.
Police say Hernando Garcia Morales, 40, from Palisades Park threw a rock at the vehicle just before the Teaneck Road exit.
He has been charged with aggravated assault, possession of a weapon for an unlawful purpose, endangering the welfare of a child, criminal mischief, resisting arrest by flight, and hindering.
Police said he was arrested at a self-made campsite within Old Croaker County Park in Bergen County.
During the investigation, police were able to link Garcia Morales to multiple rock-throwing incidents in Bogota Borough, Bergen County.
The rock shattered the glass and struck the 8-year-old girl in the head.
Authorities say no one else on the bus was injured.
The Jewish Federation put out a statement that said in part it is aware of the incident and closely monitoring the situation.
Officials say there were no markings on the bus identifying it as a Jewish school bus, so the exact motive is still under investigation.
The young girl had surgery and is expected to be OK.