Hospital officials said the civilian was a 16-year-old boy.
An Israeli military spokeswoman confirmed there had been an air strike on Palestinians as they fired a rocket from northern Gaza at Israel. She had no further details.
Israel has come under growing international pressure to reduce its military raids in Gaza since 19 Palestinian civilians, including women and children, were killed in an artillery barrage fired at the town of Beit Hanoun last week.
The army, which says the shooting was aimed at preventing militant rocket attacks on Israel, said the deaths were caused by a technical malfunction.
Israel launched a major offensive in Gaza last June after Palestinian gunmen abducted an Israel soldier and killed two others in a cross-border raid.
The military assault, also aimed at stopping the rocket fire, has killed more than 370 Palestinians, around half of them civilians, Palestinian hospital officials say. Three Israeli soldiers have been killed in the operation.
REUTERS AKJ PM1442