The target was Ahmed Sa'ad, whom the Israeli Defense Forces described as a key figure in recent rocket attacks launched from Gaza against the Israeli city of Ashkelon.
It was not immediately clear if Sa'ad was killed or injured in the strike.
"The [Israeli military] takes any fire on Israeli territory seriously, and will continue to take strong action against any attempt to carry out terrorist activity," the military said in a written statement. "We are ready and willing to defend the citizens of the state of Israel."
The Israeli broadcaster Arutz Sheva said the strike was among several so-called terrorist sites in Gaza that were hit by Israeli warplanes overnight.
The Palestinian news agency Ma'an counted a total of three Israeli air attacks in Gaza. One of them targeted a man on a motorcycle in the northern Gaza Strip. The man was seriously injured as was a 12-year-old boy who was in the area, the agency said.