Along with Gaza's Hamas-run public schools, the scores of schools run by the United Nations re-opened their doors to the 200,000 children who attend them, and had been absent for nearly a month.
"Of course, the first thing we have to do is a roll call to see who has, and who has not, survived the conflict," said UN spokesman Chris Gunness.
In the UN's Fakhoura Elementary school in the northern Gaza Strip town of Jabaliya, three chairs in an eighth-grade class were adorned with the names of students who were killed during the offensive.
Palestinian Education Ministry officials said most of the children were still in shock after having survived numerous air strikes, and many had lost friends and family members to the fighting.
Dozens of the 221 UNRWA schools in the Strip were damaged during Israel's military operation, and two of them remain unusable. A spokesman for the UN organization said students of those schools have been referred to other facilities.
AP contributed to this report