Saheeb Abu Kashef, 16, died late Saturday after being shot on August 3 east of Khan Yunis in the southern Gaza Strip, according to the ministry, AFP reported on Sunday.
Israel maintains a crippling blockade of the Gaza Strip which critics say amounts to collective punishment of the impoverished enclave's two million residents.
Protesters gathered on Friday under the slogan of "Resistance is our Choice" marking the 25th consecutive week in which Palestinians gather at the fence in the so-called Great March of Return protests, which have seen 178 Palestinians killed by IDF fire.
Another Palestinian, 28-year-old Hashem Hassan, said he saw Abdel-Al being shot 70 metres from the fence: "He threw a few stones, which flew just a few yards".
An Israeli army spokesman confirmed in a press statement that around 13,000 Palestinians joined Friday's protests in eastern Gaza, adding that its tanks targeted military facilities belonging to Hamas in eastern Gaza Strip.
The boy, named as Shadi Abdel-Al, is the youngest fatality so far from Israeli gunfire. One Israeli soldier has been killed over the same period.
The portion of the money involving Palestinians in the occupied West Bank and Gaza Strip was being redirected to programmes between Jewish and Arab Israelis, a USA embassy official said.More news: Putin inspects war games, vows to beef up army
Meanwhile, mass protests continued on Saturday in various places in the Gaza Strip.
Jewish groups from across the political spectrum are expressing mourning for Ari Fuld, 45, who was killed in a terrorist.
Romano was initially taken to a West Bank police station where he briefly met with activists from an Israeli-Palestinian group, Combatants for Peace.
Current and former United States ambassadors to Israel offered high praise in honor of an Israeli father of four murdered in a terror attack on Sunday.
Israeli security personnel work at the scene of a stabbing attack near a mall in the Gush Etzion Junction in the occupied West Bank, September 16, 2018.
Surveillance footage shared on news sites and social media showed the assailant approaching an older man near the mall entrance and stabbing him several times.