“Their bravery and dedication will always be remembered,” she said.
“I extend my earnest wishes for a swift and smooth recovery to all those who have been injured. You are in my thoughts and prayers during these challenging times.”
Trump, who advocates for children in her official role, also said: “The US stands with all of the children throughout the world. I hope soon peace will be yours”.
The plan for her to chair the meeting was announced late last month.
UN Under-Secretary General Rosemary DiCarlo said during the meeting that “when conflicts erupt, children are among those most severely affected”.
“We have been reminded of this truth over the last two days,” she said.
“Schools in Israel, the United Arab Emirates, Qatar, Bahrain and Oman have closed and moved to remote learning owing to the ongoing military operations in the region,” she added.
She also cited the reports from Iran about a elementary school strike.
Iranian officials say a strike hit an elementary school in the town of Minab on Saturday, killing 153. Iran has blamed the US and Israel.
Before Monday’s meeting began, Iran’s ambassador to the UN Amir Saeid Iravani said “it is deeply shameful and hypocritical that on the very first day of its presidency of the Security Council, the United States convened a high-level meeting on protecting children”.
The US military’s Central Command has said it was looking into reports of the incident, while Israel’s military said it was “not aware” of any IDF operations in the area.
US Secretary of State Marco Rubio said on Monday that “the United States will not deliberately target a school.”