The 15-year-old was found shot by the border fence near Gaza's long-idle Dahaniyah Airport, Ynetnews.com reported Tuesday. The boy was pronounced dead at a hospital in Rafah.
Israeli military officials said they had no knowledge of the shooting.
Israeli solders had shot at the legs of Palestinian protesters when they refused to leave two areas near the border fence, but it did not appear anyone had been hurt or killed, the military officials said.
Tensions along the border increased after the deaths last week of two Israeli soldiers and two Palestinian militants. Israeli tanks and bulldozers briefly entered the Gaza Strip and then withdrew.