An Israeli military source said the soldiers had responded after coming under fire, but Palestinians said the protesters were only throwing stones.
Palestinian witnesses said the soldiers had come under a hail of stones thrown from rooftops as they were searching for resistance fighters in the camp.
The troops opened fire killing Ibrahim Muhammad Ismail, 12, medics at a hospital in Jenin said.
The military source said soldiers had opened fire during protests by hundreds of Palestinians against a raid in the northern West Bank camp, but could not confirm whether anyone was shot.
The clashes erupted amid fears of a power vacuum in the Palestinian territories with ailing Palestinian President Yasir Arafat absent for the first time in a decade, after being flown to Paris on Friday for medical treatment.
Elsewhere in the West Bank, three Palestinian fighters shot and slightly wounded a security guard near the Jewish settlement of Psagot, outside the town of Ram Allah, and then fled the scene, an Israeli military spokesman said.