The Israeli occupation soldiers stationed at the border shot Azzam Hilal Oueida, 14, in the head while participating in the Great Return March protests near the fence to near the town of Khazaa, east of Khan Younis in the south of the Gaza Strip, Palestinian news agency (WAFA) reported.
The military also says Hamas is using the protests as cover to damage the border fence and prepare to infiltrate and carry out attacks.
More than 300 others have been hospitalised for gunshot wounds and the effects of tear gas, the ministry says.
In what the military said was a direct response, Israeli warplanes on Friday night attacked "six military targets belonging to the Hamas terror organisation's naval force in the Gaza Strip". More than 1,600 have been injured. 175 of the wounded Palestinians were injured in Northern Gaza, 251 in Gaza city area, 200 in Central Gaza, 146 in Khan Younis and 183 in Rafah.
It said several Palestinians were attempting to cross by force and troops "had operated in accordance with the rules of engagement", adding that protesters had hurled stones and rolled burning tires during the incident.
Oliver Sprague, Amnesty International UK's arms control director, told MEE: "It's clear that UK arms sales to Israel are increasing significantly against the continuing backdrop of Israel's ongoing serious human rights abuses against thousands of men, women and children suffering the consequences of life under Israel's cruel blockade of Gaza".
"Gaza is about to explode", a senior United Nations official warned on Thursday amid a spike in clashes on the border with Israel over the past week.
Israeli troops have killed 42 Palestinians and wounded more than 5,000 others since Gaza residents began staging protests along the border fence on March 30 to demand the right of return for Palestinian refugees.
Britain sold Israel components for the US-made Apache helicopter which have been used inside Gaza
US President Donald Trump, who tore up decades of policy by recognising Jerusalem as Israel's capital, said Friday he "may go" to the city for the embassy opening.
Zeid Ra'ad Al Hussein, the U.N. high commissioner for human rights, said Israeli troops have not heeded warnings by the United Nations and others, repeatedly using lethal force against unarmed protesters in the past month.
Owaida is the second teenager killed by Israeli fire recently, following the death of Mohhamed Ayoush, 15, last week.
The Great March of Return movement is officially scheduled to continue until May 15, known as Nakba Day, marking the expulsion of hundreds of thousands of Palestinians during the creation of Israel. "I am doubly concerned by reports of unusually severe injuries resulting from the use of live ammunition".
IDF forces responded by firing live ammunition and tear gas at demonstrators at five locations on the Gazan side.
"These trends call into question to what extent the ISF's rules of engagement, which are not public, are in line with global law, or at least to what degree the ISF abides by its own rules", said Zeid. With hooks and a long rope, the activists pulled at parts of the barbed wire adjacent to the fence.
Hamas' Interior Ministry announced that Egypt had agreed to open the Rafah border crossing for three days, beginning Saturday.
Toddler Alfie Evans dies in hospital
James, 20, posted a message on social media thanking everyone who supported the family through Alfie's illness and court fight. The Pope added: "Today I pray especially for his parents, as God the Father receives him in his tender embrace".