They said Palestinian witnesses had reported that he had been shot from a passing car.
Fourteen people were wounded, according to Palestinian witnesses and hospital officials.
A 10-year-old girl was killed, while her parents and a teenage sister were wounded, Palestinian witnesses said.
Two other youths were injured in the clash, Palestinian witnesses said.
A 12-year-old boy hit by shrapnel died later, Palestinian witnesses said.
Palestinian witnesses said the boy had been shot at close range after he was pushed to the ground.
Palestinian witnesses said four students, including one woman, were taken to a hospital with gunshot wounds.
But an initial investigation indicates that the Palestinian witnesses were correct.
Palestinian witnesses said one man was shot dead while throwing stones.
Palestinian witnesses said the gunmen had gone there with wounded colleagues.