The teenager is accused of being in the car with another occupant and shouting abusive comments as it went past Our Lady of Lebanon Church and the Maronite College of the Holy Family (MCHF) on 16th September.
He has been charged with intimidating a school staff member and offensive conduct, and will appear in a child's court in October.
Speaking on behalf of the school, Joseph Wakim, told the Daily Mail Australia the arrest would give parents and students peace of mind.
"My daughter was very concerned that an overseas group making front page news every day could be at the front door of her school," he said.
In a statement, Our Lady of Lebanon Church parish priest Mons Shora Maree said: "On Tuesday afternoon there was a single incident [whereby] a verbal threat was made by a single passing motorist to...MCHF College staff members.
"The incident was reported to police who swiftly attended.
"This is now in the hands of police who are fully investigating. Please do not respond to or circulate any other version of the truth on social media as it creates unnecessary panic."