Youssef al-Anati said his 11-year-old nephew, Khalil, was shot dead even though he was not taking part in the disturbances near the city of Hebron. The boy was taken to a local hospital, which said he had been hit in the back with a live bullet.
"Khalil was standing outside and at a distance some kids were throwing stones at the Israeli army," al-Anati told Reuters. "Suddenly Khalil collapsed to the ground and we rushed to him; he was all covered in blood."
In response the IDF, said that during riots in the village "if forces opened fire, as a result of which a Palestinian minor was killed. The IDF regret his death. The IDF will investigate the incident and an internal investigation (into the soldiers' conduct) will be opened."
Tensions in the West Bank have run high during Israel's more than month-old war with Islamist militants in the Gaza Strip, another territory where Palestinians seek statehood.
IDF troops killed one Palestinian and wounded dozens of others protesting against the army's Gaza campaign on Friday in the West Bank, Palestinian medical officials said.
The person killed was Ahmed al-Qatari from the Al-Amaari refugee camp near Ramallah. The 19-year-old Palestinian was killed in clashes near the Psagot settlement between Jerusalem and Ramallah.
AFP contributed to this report