The Palestinian Ministry of Health identified the victim on Sunday as Omar Mohammed Rabea, and said he was shot near the town of Turmus Aya, northeast of the city of Ramallah.
The Israeli military said it had killed a “terrorist” who was throwing stones.
The attack comes amid a sharp rise in Israeli violence against Palestinians in the occupied West Bank.
According to Wafa, Israeli officials arrested Rabea, later pronouncing him dead, and have withheld his body.
Two other Palestinian boys, aged 14 and 15, were shot in the attack that killed Rabea, the agency reported. The boys, who hold United States citizenship, were wounded in the abdomen and the thigh and were transferred by the Palestinian Red Crescent Society (PRCS) to a hospital for treatment.
The Palestinian foreign ministry meanwhile condemned the incident as an “extra-judicial killing” by Israeli forces during a raid in the town, saying it was the result of Israel’s “continued impunity”.
Earlier reports from the town’s mayor suggested it was an Israeli settler who had fired the bullets.
There have been several cases of US citizens being killed by Israelis in the occupied West Bank.
In 2024, Aysenur Ezgi Eygi, a 26-year-old Turkish-American activist, was shot in the head by an Israeli soldier while protesting against illegal Israeli settlements, according to witnesses.
Shireen Abu Akleh, a Palestinian-American journalist for Al Jazeera, was also killed by the Israeli military in 2022 while reporting in the occupied West Bank, despite being clearly identified as a member of the press.