On Friday, hundreds of Palestinians converged on the border area to take part in weekly demonstrations against Israel's decades-long occupation.
Israeli military spokesman Avichay Adraee said on Twitter that, according to "indications" and unnamed "witnesses", the boy was killed after being hit by stones that had been thrown.
"It was unsurprising to us the Trump administration gave us only two choices: either we lose our relationship with the administration or we lose our rights as a nation", he said. Incendiary balloons have become a common terror tool in Gaza, with cheaply made balloon and kite arson devices having ignited more than 8,000 acres of Israeli land since March.
The youth was reported to be in moderate condition.
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A group of Palestinian women wave the Palestinian flag during a March 30, 2018 protest in Gaza. "This Friday was his destiny to die as a martyr", said the boy's father, Abdel-Aziz Abdel-Al. Almost 20,000 Palestinians have also sustained injuries.
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A Palestinian boy holding his national flag looks at clashes with Israeli security forces near the border between the Gaza Strip and Israel east of Gaza City on May 14, 2018, as Palestinians protest over the inauguration of the U.S. embassy following its controversial move to Jerusalem.
Friday's dead, one of them a boy whom medics said appeared to be around 14 years old, brought to 177 the number of Palestinians killed since the sometimes violent protests were launched on March 30 to press several demands against Israel.
Israel accuses Hamas, the movement that runs the Gaza Strip, of seeking to use the protests to carry out attacks or infiltrations. Hamas has denied this.
Earlier, the IDF said an explosive device was uncovered on Friday morning by IDF troops adjacent to the security fence in the southern Gaza Strip and was disposed of safely.
Israel maintains a crippling blockade of the Gaza Strip it says is necessary to isolate Hamas, which whom the Jewish state has fought three wars since 2008.
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