Rifat Abu Amra was killed on Sunday evening as he walked through the streets of Rafah's refugee camp.
An Israeli bullet passed through the 28-year-old's neck and lodged in his head, according to Palestinian medical sources.
His death brings to 4152 the number of people killed since the start of the Aqsa Intifada that began in September 2000 - 3156 of whom were Palestinian.
Just hours earlier, Israeli helicopter gunships launched missiles in Gaza City and in the Nusairat refugee camp, badly damaging several workshops.
The first strike struck the northern part of Gaza City, while the second missile landed in the south-eastern Zaitun district.
A third missile was also fired on the Nusairat refugee camp south of Gaza City.
No casualties were reported from any of the strikes, but several of the buildings in industrial areas suffered extensive damage.
More Palestinians killed
Earlier, a young Palestinian stonethrower was killed by Israeli occupation soldiers in the northern Gaza Strip.
The victim died when soldiers opened fire in the direction of the stonethrowers, witnesses said on Sunday.
The young man, aged 18, was hit by a bullet in the neck and died in a nearby hospital, the medical source said.
An Israeli military source said: "A violent disturbance broke out in Bait Hanun which troops could not control, so they fired towards the group leader and hit him."
The deaths follow yesterday's killings of two Palestinian boys, aged nine and 15, in confrontations with stone-throwing protesters.
Violence has surged in Gaza since Israeli Prime Minister Ariel Sharon said he planned to pull out soldiers and settlers by the end of next year, as Palestinian resistance groups and the army vie for supremacy before a withdrawal.