The violence was also a sign of the growing escalation in the West Bank as Israel's search for the three Jewish seminary students entered its second week. The teen killed Friday was the second Palestinian shot dead by Israeli troops this week.
Israel has blamed the Islamic militant Hamas group for the apparent abduction, but has offered no proof.
Israeli Prime Minister Benjamin Netanyahu has used the search to promote two other objectives — a new crackdown on Hamas and an attempt to discredit the Palestinian unity government formed earlier this month by Western-backed Palestinian President Mahmoud Abbas and supported by Hamas.
Hamas has praised the abduction of the teenagers but has not claimed responsibility for it. The group has abducted Israelis in the past to press for the release of thousands of Palestinians held in Israeli prisons.
Over the past week, thousands of Israeli troops have searched hundreds of locations in the West Bank and arrested more than 300 Palestinians, many from Hamas.
The Israeli military said it conducted raids in four towns and refugee camps early Friday, detaining 25 suspects and searching about 200 locations. The army said nine institutions linked to Hamas were searched and materials were confiscated.
In one raid, in the town of Dura near Hebron, Palestinian youths threw stones at soldiers, drawing army fire. A hospital official, who spoke on condition of anonymity because he was not authorized to talk to media, said 15-year-old Mohammed Dodeen was killed by a bullet in the chest.
The army also opened fire during a raid in the Qalandiya refugee camp, where three Palestinians were seriously wounded, said Ahmed Bitawi, director of Ramallah hospital. He said one of the wounded was in the intensive care unit and two were in serious condition.
The army confirmed soldiers used life fire, saying they were responding to life-threatening situations, and added that the troops engaged in sporadic confrontations during Friday's raids.
Palestinians threw home-made explosives, firebombs, fireworks and stones at the forces, the military said. In Qalandiya, a soldier was lightly hurt by a grenade thrown at troops, it said.
The military also said it carried out airstrikes on in Gaza overnight, in retaliation to several rockets fired by Gaza militants at Israel. The army said it targeted sites from where rockets had been launched and a weapons storage facility.
Gaza Health Ministry spokesman Ashraf al-Kidra said six people were lightly hurt in the airstrikes, including four children.
Since the escalation erupted over the teens' disappearance, 16 rockets have been fired at Israel, the army said. A house was damaged but there were no injuries.
The three teens disappeared June 12th while hitchhiking home. There has been no sign of life from the missing teens or any ransom or other demands from their purported kidnappers.
In Israel, prayer vigils and round-the-clock media coverage have followed the teens' disappearance.