A missile missed the vehicle and hit a nearby home instead, wounding the child on Monday.
The house itself, in the West Bank town of Jenin, was severely damaged.
Two wanted members of the Palestinian resistance group, al-Aqsa Martyrs Brigades, escaped uninjured from the strike.
One of those in the vehicle has been identified as Mahmud Abu Khalifah, a local al-Aqsa leader.
The al-Aqsa Brigades is an armed offshoot of Palestinian Authority chairman Yasir Arafat's Fatah movement.
There was no immediate comment on the strike from the Israeli military.