The three, who the Gazan health ministry said were aged 13 and 14, were killed late on Sunday near the tense border between the Hamas-run Gaza Strip and Israel.
Ashraf al-Kidra, a health ministry official, reports that ambulance personnel are carrying corpses to a hospital, having recovered them from within the perimeter fence that separates Gaza from Israel.
In response to Hamas' "grave actions", dozens of IDF fighter jets, attack helicopters and aircraft struck roughly 80 Hamas targets throughout the Gaza Strip, said the Israeli army.
The boys' bodies were wrapped in Palestinian flags and carried by mourners who shot in the air as they chanted "God is Great".
Alon Schvartzer, director of Policy for Im Tirtzu, said that they arrived to show solidarity with the people of the south. It gave their ages as 14 and 15.
Ibrahim al-Satari, the father of 13-year-old Mohammed, said he couldn't understand it.
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The settlers were protesting against "tensions in (Gaza Strip)" and the Israeli security cabinet's decision not to respond to the recent security escalation and rocket fire from Gaza.
More specifically, regarding the weekly Hamas-led border protests, just 36 percent of Gazans support this tactic, while 62 percent say they oppose it.
Palestinians and rights groups say protesters have been shot while posing little threat.
According to the spokesman, they were burning tyres as well as hurling rocks and explosive devices toward soldiers and at the fence between Israel and the blockaded Palestinian enclave.
Since the rallies began on March 30, more than 200 Palestinians have been martyred- and thousands more injured - by Israeli troops deployed along the other side of the buffer zone.