"The two children, Adam Samer Al-Ghoul (8 years old) and Basil Suleiman Abu Al-Wafa (15 years old), were shot dead by occupation forces in the city of Jenin," the Palestinian health ministry said.
The Islamist movement Hamas claimed Al-Wafa as a member.
Unverified video circulating on social media appeared to show the 8-year-old being hit but the footage did not show who fired the shot.
Asked to comment on the footage, the Israeli military said: "Earlier today, during IDF activity in the Jenin Camp, a number of suspects hurled explosive devices toward IDF soldiers. The soldiers responded with live fire toward the suspects and hits were identified."
The raid into the Jenin camp, one of the most active centres of militant activity in the West Bank which was heavily damaged by a major Israeli operation in July, left piles of smashed rubble and damaged houses.
WAFA said Palestinians Muhammad Jamal Zubaidi and Wissam Ziad Hanoun from Jenin camp were killed by Israeli forces, adding that "the occupation forces took their bodies".
The Israeli army said in a statement Zubeidi and Hanoun were killed during "counterterrorism activity conducted in the Jenin Camp" jointly by the military, national security agency and border police.
Zubeidi was a senior Islamic Jihad operative and one of the central leaders in the Jenin Camp, the army said.
The Israeli military said he had been involved in extensive militant activity and carried out shooting attacks and promoted other attacks.
(Reporting by Ali Sawafta, Writing by Clauda Tanios, Editing by Andrew Heavens, Alexandra Hudson and Cynthia Osterman)
