About 8,000 Palestinians gathered near the border fence, the Israeli military said. Most kept their distance, while some burned tires and tried to throw an explosive device into Israel, though it did not land across the border, the military said.
A military spokeswoman said the troops responded with “riot dispersal means” and fired in accordance with Israeli procedure.
Gaza’s health ministry said 16-year-old Mohammad Jahjouh was fatally shot in the neck, while 25 others, including a local journalist, were wounded by Israeli gunfire.
It later said two men, aged 28 and 40, died of injuries they sustained at protests in two separate locations along the fence with Israel earlier in the day.
Health officials in Gaza, which is run by the Hamas terror organization, say more than 220 Palestinians have been killed since they began weekly March of Return border protests on March 30 to demand the easing of Israel’s blockade on the territory.
Alarmed at the bloodshed, Egypt, the United Nations and Qatar have sought ways to improve conditions in the enclave.
Israel withdrew settlers and soldiers from Gaza in 2005 but maintains tight control of its land, air and sea borders. The wider Israeli-Palestinian peace process has been stalled for several years.