Ali al-Awour was wounded in Wednesday's strike targeting his uncle, radical Salafist Mohammed al-Awour, who was killed. Another Palestinian man was wounded.
The Israeli military said on Wednesday it had targeted "terrorists affiliated to the international jihad", its designation for Al-Qaeda inspired groups in Gaza.
Awour, 30, and the wounded man were travelling on a motorbike when they were attacked. The boy had been passing by on foot.
Awour had been involved in rocket attacks on southern Israel in recent years and particularly over the past month, an Israeli army statement said.