The ministry said 15-year-old Mohammad Balhan sustained gunshot wounds to his head, chest and abdomen.
In a separate part of the West Bank, thousands of Israelis, including government ministers, marched towards the evacuated outpost of Evyatar in support of settlement expansion.
Palestinians want an independent state in the West Bank and Gaza with East Jerusalem as its capital – territories Israel captured in a 1967 war.
US-sponsored statehood talks have been stalled since 2014 while Jewish settlements have expanded, developments which Palestinians say have undermined the chances of a viable state being established.
Source: Israeli forces kill Palestinian teen in West Bank raid