Luaye al-Burnu, a local official in the Izz al-Din al-Qassam Brigades responsible for manufacturing weapons, died in the attack early on Saturday morning, a medical official told AFP news agency.
Two other people were wounded when the minivan they were travelling in was attacked in Gaza City.
Abu Obeida, a spokesman for Hamas, told the Associated Press news agency that the three men in the vehicle were all fighters with the Izz al-Din al-Qassam Brigades.
The Israeli army confirmed the attack.
Hamas gunmen also attacked a house used by Israeli soldiers, setting off explosives and firing rockets, Abu Obeida said. One gunman was killed in the fighting there, he added.
An Israeli sniper shot dead another gunman.
In Beit Hanoun, the body of a 46-year-old man was found under the rubble of a house after an air strike, rescue workers said.
At least 10 other people were wounded in missiles strikes during the night, Palestinian hospital officials said.
Eight other Palestinians died in air strikes overnight in the towns of Beit Hanoun, Beit Lahiya, Jabaliya and Rafah, at least five were Palestinian fighters, including one Hamas security officer who was killed when his car was hit in Rafah.
Early on Saturday, military bulldozers began demolishing homes near a mosque in Beit Hanoun where two women were killed by the Israeli military the previous day. Witnesses said residents received no warning and were seen running for safety.
On Friday, hundreds of Palestinian women had streamed to the Al-Nasir mosque to help free about 60 people who had been trapped inside by Israeli troops. Men carrying arms were said to be among those inside the mosque.
Israel has intensified its military operations in Gaza in an attempt, it says, to prevent makeshift rockets from being fired into Israel and to pressure the Palestinians to hand over a solider who was captured earlier in the year.
At least 38 Palestinians, about half of them civilians, have been killed by Israeli fire since Wednesday.
Members of the Palestinian factions have sought the release of some of the thousands of Palestinians held in Israeli jails in exchange for the Israeli soldier.