Muhammad Jabir Sayyid, 16, was shot as he was throwing stones at soldiers near a road running through the West Bank, Palestinian sources said on Thursday
Israeli military sources said some Palestinians had tried to block the road, used by Jewish settlers, with rocks and a metal bar.
Sayyid was transferred by the army to the Bellinson hospital near Tel Aviv, said the hospital spokesman.
His death brings to 3683 the number of people killed since the start of the Intifada in September 2000, including 2757 Palestinians and 860 Israelis, according to an AFP count.
Also on Thursday, an al-Qassam rocket was dropped on the Israeli city of Sderot, Israeli military sources said.
The rocket was launched form the Gaza Strip. No casualties were reported, the sources added.