Wednesday from the wounds he sustained, the Palestinian health ministry said.
The 15-year-old was shot in clashes at the entrance of Al-Bireh, north of Ramallah in the West Bank, the ministry said in a statement.
The health ministry did not say what day the teen was wounded, but the official Palestinian news agency WAFA said he was shot in the stomach during clashes on May 15.
The Israeli army said it was looking into the incident.
Major protests took place across the Palestinian territories on May 14 as the United States transferred its Israeli embassy to Jerusalem from Tel Aviv.
Smaller protests took place on May 15, which was the 70th anniversary of the Nakba, or catastrophe, when hundreds of thousands fled their land during the war surrounding the creation of Israel.
More than 60 Palestinians were killed in clashes along the Gaza border over the two days, but the teen who died on Wednesday was the first killed in the West Bank.
Palestinians see the eastern part of Jerusalem as their capital and the embassy move led the Palestinian leadership to cut ties with US President Donald Trump's administration.
Guatemala and Paraguay have followed in Washington’s footsteps by opening their embassies in Jerusalem.
US President Donald Trump’s decision to relocate the embassy drew international condemnation and the Israel crackdown on the protesters has prompted calls for an independent probe.
The international community has condemned Israeli troops for using live ammunition against unarmed Palestinians.
