The missile landed near two cars in north Gaza that carried militants from al-Aqsa Martyrs Brigades, part of Palestinian President Mahmoud Abbas's Fatah faction, and from Islamic Jihad, which killed five Israelis in a suicide bombing on Wednesday.
The Israeli army said it had been targeting militants who were en route to a rocket launch pad near the northern Gaza town of Beit Hanoun.
Palestinian medics said the attack near Beit Hanoun destroyed the two vehicles and killed an al-Aqsa militant, while the rest of the men seemed to have escaped unharmed.