STORY: At least six other Palestinians, including two journalists, were wounded by Israeli fire, medics at the scene said.
Palestine TV released footage of the scene, with audio of journalists shouting as one of them was hit by gunfire.
The Israeli military did not immediately respond to a request for comment on Wednesday, a national holiday in Israel.
The clashes began when Israeli forces surrounded the house of Salman Imran, who the Islamist militant group Hamas claimed as a member, in the town of Deir al-Hatab east of Nablus.
Witnesses said dozens of Palestinian gunmen fired at Israeli forces in an attempt to foil their operation.
The Palestinian Health Ministry said the man who was killed, 21-year-old Alaa Zaghal, was shot in the head.
Palestinian medics said he was unarmed when Israeli forces fired at him near the town's entrance, away from where the clashes were taking place.
The Israeli military has intensified its raids in the West Bank in recent months following a spate of Palestinian street attacks that killed 19 people in Israel and as a general election approaches on Nov. 1.
More than 80 Palestinians, including gunmen and civilians, have been killed since January, in what the European Commission described as the deadliest year in the West Bank since 2008.