Two girls were also wounded in the incident on Friday, which the army said was caused by an accidental discharge of a machine-gun manned by a soldier who was on top of an armoured vehicle.
"One boy was killed and two girls were wounded," an army spokesman told AFP.
"We express our regrets and an inquiry has been launched."
The youngster, named as Mahmud Qabha, was killed near a checkpoint located to the west of Jenin and close to a new security fence which is being built by the Israelis across the West Bank.
The boy's grandfather told AFP that he had parked his Mitsubishi jeep some 200 metres (yards) away from the tank when shots rang out without warning.
"Immediately the tank shot without any warning. The bullets cut through the head of my grandchild," Mustafa Atatra told AFP.
"About 16 bullets went into the car. My wife was also wounded in the leg."
Bartaa's mayor Ghassan Kabaha told AFP that the other two children, aged six and seven, had been injured in the incident and taken to hospital.
Witnesses said they had been driven in an army ambulance.
A pool of blood could be seen on the seat and floor of the blue and grey-coloured jeep which was still parked at the scene of the shooting. Its windows had been shattered.
As news filtered through to locals, scores gathered at the scene to remonstrate with the army.
Some angrily accused soldiers of "killing our children" while others attempted to rush at the soldiers but were held back.
The atmosphere in the area has been soured by the construction of the fence which takes the form of a concrete wall around Jenin, regarded as a key staging post for Palestinian militants intent on inmflitrating Israel.
Palestinian prime minister Mahmud Abbas, currently in Washington, was expected to call for the scrapping of Israeli army checkpoints in the West Bank and a halt to the building of the fence in talks later Friday with US President George W. Bush (news - web sites).
An Israeli border guard on Thursday shot and killed a Bedouin carrying illegal Palestinian workers in his vehicle in southern Israel.
After the shooting of the Bedouin, named as 23-year-old Mohammed Bau al-Jihan, dozens of members of his tribe threw stones at the police near the scene of the incident in the Negev, injuring one.
