The strike targeted Mahmoud Hamdan Samiri, a Khan Yunis resident Israeli authorities said was involved in the terror cell behind Tuesday's attack at the Kissufim crossing in which an Israeli soldier was killed and three others were wounded, The Jerusalem Post reported.
The airstrike occurred after Palestinians fired a rocket that landed in an open area near Sderot, the Post said. No injuries or damage was reported.
The rocket attack came after an Israeli jet fired on a weapons manufacturing plant in the Rafah area Wednesday in response to a rocket-firing from the Gaza Strip hours earlier.
The airstrike was Israel's first attack on a building inside Hamas-controlled Gaza since the sides declared cease-fires ending their three-week battle.
Israeli Foreign Minister Tzipi Livni said after Wednesday's rocket firing that Israel would respond to all acts of aggression.
The Israeli government backed Livni's position in a statement saying the Israeli military "will respond to any terror attacks in accordance with decisions made by the Israeli government."
Also on Wednesday, Israeli Defense Minister Ehud Barak said he canceled a visit to the United States to meet with Defense Secretary Robert Gates to oversee developments in Gaza.