Eyewitnesses said on Thursday that it was the worst violence in days.
Nablus city medics said the boy was shot in the head when soldiers confronted stone-throwers during a raid against resistance fighters in the city.
They said the boy was dead by the time he arrived at a local hospital.
At least one other person was wounded in the incident, they added.
In a separate raid near the town of Bethlehem, soldiers shot and killed a 22-year-old man and wounded three other people, medics said. They gave no information on the circumstances of the incident.
An Israeli military source said soldiers opened fire on Palestinians who threw firebombs at them in both Nablus and Bethlehem, and saw one person being hit in each incident.
Earlier on Thursday, about a dozen people were wounded when Israeli occupation troops fired rubber bullets to disperse demonstrators protesting against the illegal barrier Israel is building in the occupied West Bank.
The army said soldiers used tear gas in the clash at a village of Zawiyeh on the West Bank border with Israel.
Elsewhere, soldiers raided a wedding in the city of Ram Allah, detaining the groom and two other men, witnesses said.
An Israeli military official claimed the three were activists of the Hamas resistance group and had been involved in the past in plotting bombings and shooting attacks.
More than 2,500 Palestinians and 900 Israelis have died since an uprising began after peace talks froze in September 2000.
On 6 June, Israeli soldiers shot dead a paraplegic basketball player near the Qalandia refugee camp.