An army statement said the pair attacked an Israeli patrol west of the city of Jenin with rocks before firing on soldiers with a rifle.
"The force responded to the shooting and fired towards the attackers, resulting in their deaths," it said.
The Palestinian health ministry named those killed as Nihad Waked and Fuad Waked, both 15 years old. They were not thought to be closely related.
Since the current round of bloodshed erupted at the beginning of October, 169 Palestinians have been killed by Israeli forces. Most were carrying out attacks but others died during clashes and demonstrations.