An Israeli army spokesman said Israeli troops clashed with Palestinian fighters during the raid on a house in the southern Gaza village of Abasan near the town of Khan Yunus on Thursday.
Witnesses said an Israeli helicopter fired two missiles.
Israel launched an air and ground offensive in the Gaza Strip in late June after fighters, including from Hamas, killed two Israeli soldiers and abducted one in a cross-border attack.
Family members said the Palestinian man killed on Thursday was Youssef Abu Daqqa, the brother of Younis Abu Daqqa, a prominent member of Hamas in southern Gaza. Younis was detained.
As part of its offensive, Israel has detained dozens of leading Hamas officials in the past two months, including cabinet members and legislators in the occupied West Bank.
Jihad leader shot
On Wednesday, a top Palestinian armed faction leader in the West Bank was shot in the head and seriously wounded, fighters and hospital officials said.
Aljazeera said Husam Jaradat, the West Bank leader of Islamic Jihad's military wing al-Quds Brigades, sustained serious injuries after Israeli soldiers attempted to assassinate him in Jenin's refugee camp.
Medics said he was taken to hospital and was in critical condition.
An Israeli undercover unit stormed the camp, broke into a house and opened fire at Jaradat, Aljazeera said.
But Islamic Jihad said they were not sure Israel was behind the shooting. The Israeli army said it was checking the report.
Late on Wednesday, an Israeli tank fired a shell at two men who approached Gaza's border fence with Israel near Abasan, according to Palestinian officials and the army.
Israel has killed more than 200 Palestinians - most of them resistance fighters - since the offensive began two months ago. Palestinian officials fear that Israel, after battling Hezbollah fighters to a stalemate in Lebanon, will now turn its full attention back on Gaza.