"Mohammed Yehya, aged 18, died in Nablus hospital after being shot in the leg yesterday (Monday) night during an Israeli army operation in Araqa village west of Jenin," a medical source said.
The Israeli army said troops had opened fire on a group of Palestinians who were seen trying to cross the barrier close to the Jewish settlement of Shaked.
"Yesterday, a group of Palestinians was spotted trying to cross the security fence near the community of Shaked not far from Araqa village," a military spokeswoman said.
The military prosecutor has opened an inquiry, she added.
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The separation barrier is a vast structure, most of it built inside the occupied West Bank, that divides Israel and its main settlement blocs from the rest of the territory.
Israel refers to it as the "security fence" and insists it is crucial for keeping out would-be attackers.
The Palestinians have branded it the "Apartheid wall," and say it is a thinly disguised land grab aimed at stealing part of their future state.