The Israeli army also bulldozed the main street in the Nur Shams refugee camp in a separate operation, Palestinian officials said, highlighting a spike in tensions since the Gaza war erupted on October 7.
Ghassan Gharib Zahran "was martyred by occupation bullets" at Deir Abu Mishal, near Ramallah, a health ministry statement said.
The Israeli army told AFP that "terrorists threw stones at Israeli vehicles in the Deir Abu Mishal area".
Troops "responded by opening fire... which led to the injury of one of the terrorists", the army added in a separate statement.
The boy's cousin, Munther Zahran, said the dead boy was hit by a "bullet in the stomach" while he was in the main street in Deir Abu Mishal.
"The road is used by settlers and the army is constantly monitoring it," he added.
Occupied by Israel since 1967, the West Bank has seen an escalation in violence since the Hamas attack on southern Israel set off a bitter conflict in the Gaza Strip over nine months ago.
At least 572 Palestinians have been killed in the West Bank by Israeli troops or settlers since October 7, according to Palestinian officials.
The Nur Shams camp, near Tulkarem, has also been the target of several army operations in recent weeks.
Army bulldozers tore up the camp's main street and destroyed several buildings on Tuesday, an AFP journalist saw.
Palestinian Authority prime minister Mohammed Mustafa said there would be major "humanitarian repercussions" from the Israeli action.
"Recent events have shown the unprecedented destruction of essential infrastructure, including the water and electricity networks, and significant demolition" of Palestinian homes, Mustafa said in a statement.
