The Palestinian Ministry of Health said that Marwan Barbakh, 13, and Khalil Othman, 15, were shot dead during a protest in the east of Khan Younis.
At least 15 others were injured during the protest, the ministry said without providing further details, Ma'an News Agency reported.
The Palestinian Red Crescent later said that its ambulance crews had treated seven Palestinians shot with live rounds across the Gaza Strip, in addition to 21 who suffered excessive tear gas inhalation.
Earlier Saturday, Hamas spokesman Sami Abu Zuhri condemned the international community for remaining silent about Israeli war crimes.
He blamed Israel for committing war crimes against the Palestinian people "through the execution of young Palestinian men and women at the scene of action."
The two boys' deaths come after seven Palestinians were killed when Israeli snipers opened fire on demonstrations near Gaza's border fence on Friday, also east of Khan Younis.
According to the Palestinian Ministry of Health, Israeli forces injured 145 other Palestinians by live fire or rubber-coated steel bullets during the protests.
The two boys' deaths brings the total number of Palestinians killed by Israel's army to 20 since fierce clashes swept the occupied Palestinian territory on Oct. 1, with around 1,000 injured with live and rubber-coated steel bullets in the same period.
The Israeli army has come under repeated criticism over its violence toward children.
Defense for Children-Palestine said in a report last month that Israeli forces and Jewish extremists had killed at least 1,991 children since 2000.
Among those, 535 children were killed directly by Israeli attacks during the 2014 offensive on Gaza, nearly 70 percent of whom were under the age of 12.
A further 3,306 children were injured during the war, including more than 1,000 who suffered permanent disability, the report said.
Following the conflict, the UN said: "There is not a single child who has not been adversely affected by the recent conflict in Gaza, where children suffer from bed-wetting, difficulties in sleeping, nightmares, a loss of appetite, and display more aggressive behavior at school."