The children, upset that Israeli soldiers searched their bags and made them lift their shirts before passing through the checkpoint on their way to school, refused to co-operate.
The group of about 300 elementary school children swarmed around the checkpoint on Tuesday, shouting: "We want freedom to study." They kicked the plastic barrier separating them from Israeli soldiers, witnesses, including an AP reporter, said.
They said troops raised their rifles but no shots were fired and no one was injured.
Soldiers scuffled with a few female pupils who confronted them, but the group scattered when soldiers fired teargas into the crowd and arrested two of them, the witnesses said.
The rest of the pupils went home as part of a strike in protest against the security checks.
The checkpoint, which has metal detectors and an X-ray scanner, is in an area where resistance activity has been high, the Israeli army said.
Soldiers used teargas to disperse the crowd because the demonstrators were pushing and shoving the soldiers and refused to undergo a security check, the army said.
But Muhammed Qawasmeh, the Palestinian Education Minister, said: "The problem is not with the students.
"The problem is the army and the checkpoints. Pupils who are six and seven years old should not have to be subjected to body searches."
He said that pupils regularly arrived late for classes and were made to stand outside in bad weather while waiting for about 800 children to clear the checkpoint every morning.