Witnesses said Israeli troops fired tear gas, rubber bullets and possibly live rounds at rock-throwing demonstrators in the village.
Another protester, aged 15, was wounded by the Israeli forces, the medics said.
About 200 people, including Israeli and foreign activists as well as Palestinians, took part in the demonstration.
Activists protesting against Israel's construction of the West Bank barrier have clashed with soldiers nearly every Friday outside Nilin and nearby Bilin for more than two years.
Israel says the projected 723km of steel and concrete walls, fences and barbed wire is needed for security.
The Palestinians view it as a land grab that undermines their right to a state.
To date Israel has built 57 per cent of the projected barrier, most of it inside the occupied West Bank.
The International Court of Justice issued a non-binding resolution in 2004 calling for parts of the barrier inside the West Bank to be torn down and for further construction in the occupied territory to cease.
Israel has ignored the ruling.