According to Aljazeera's correspondent in the area, troops in more than 20 military vehicles entered the town in the early hours of Saturday, imposing a curfew and storming some Palestinian homes.
The troops then surrounded a four-storey residential building in which Thair Abu al-Kamil, reported to be a deputy leader of al-Aqsa Martyrs Brigades, was holed up, reports Ali al-Sumudi.
An exchange of gunfire was heard between al-Kamil and the troops before bulldozers arrived and demolished the building.
Al-Kamil was trapped inside and buried alive. It took more than an hour for his body to be retrieved.
The resistance leader has been on Israel's most wanted list for more than two years.
Israeli troops withdrew from Jenin shortly after the raid.
Residents of the town have staged a demonstration in protest against the incident. In a similar manner, Israeli troops had killed al-Kamil's brother and demolished his home a month ago in the Jenin refugee camp.