The Palestinian, Ahmed Zahi Bani Shamsa, 16, was shot on Wednesday during clashes with the IDF in the town of Beita.
A few hundred Palestinians had gathered near Nablus in the northern West Bank to protest Israeli settlements.
Some in the crowd, with their faces covered by masks, threw rocks at soldiers and burned tires, witnesses said.
A spokeswoman for the Israeli army said they were checking into the report of the adolescent's death.
Tensions remain high in the region despite a ceasefire reached last week between Israel and the Palestinian terrorist group Hamas in Gaza that ended 11 days of fighting.Reuters contributed to this report.