The raid took place in the town of Qabatiyah near the city of Jenin, said Jenin governor Mohammad Abu Al-Rub who confirmed the "deaths of two martyrs".
The Palestinian Red Crescent said a third Palestinian was also killed in the raid. The Ramallah-based health ministry identified him as 21-year-old Qais Muhammad Zakarneh.
An AFP correspondent reported that the military also launched a raid in the city of Jenin itself. The military said this was part of the Qabatiyah operation in the area of Jenin.
"During the counterterrorism operation, IDF soldiers encircled a structure in which two senior wanted suspects were located in the area of Jenin," a military statement said.
"The soldiers exchanged fire with the wanted suspects, during which a number of shoulder-fired missiles were launched toward the structure.
"The two wanted suspects were eliminated and weapons were found in their possession," the military said, adding that a soldier was lightly wounded in the firefight.