Sa'ad Salah, 21 was shot in the head and killed on the spot, according to a source in a Jenin hospital, while 17 year old Aws Salameh succumbed to his wounds at the hospital early on Wednesday.
They were the 38th and 39th Palestinians to be killed by Israeli forces this year, Al Jazeera reported.
Salah's uncle told local media that the Israeli army "executed him in cold blood".
Mujahid al-Saadi, a journalist and resident of Jenin refugee camp, said that after shooting Salah in the head, Israeli soldiers then fired ten bullets in his chest.
"The army was in the city of Jenin arresting a number of Palestinians - most of whom were former prisoners - before they raided the camp," al-Saadi said.
No arrests were made in the camp, he added.
A third Palestinian was shot in the leg and is in moderate condition.
The Israeli army said soldiers shot toward "attackers" after "Palestinian gunmen opened fire at the forces and assailants hurled explosive devices at the forces" who entered the camp.
None of their forces were wounded in the incident, the army added. Stun grenades and tear gas were also fired at Palestinians in the camp.
Twenty-one Palestinians across the West Bank were arrested by the Israeli army during early morning raids, mostly for rock throwing and taking part in protests.
A wave of unrest that broke out in October 2015 has claimed the lives of 277 Palestinians, 42 Israelis, two Americans, two Jordanians, an Eritrean, a Sudanese and a Briton, according to an AFP news agency toll.
Israeli authorities say most of the Palestinians killed were carrying out knife, gun or car-ramming attacks.
Others were shot dead in protests and clashes, while some were killed in Israeli air strikes on the Gaza Strip.