Little remains of the Bamrungsart Pondok boarding school for boys in southern Songkhla province after the attack late on Saturday.
Attackers threw explosives into the building and sprayed it with bullets, police say.
Forensic experts sifted the ruins for clues to the identity of the attackers, said to be Islamic extremists.
A boy aged 12 and two boys aged 14 were killed and several pupils were wounded.
Angry villagers blamed the attack on the security forces and protested against the government.
Thai soldiers are deployed in force in the southern provinces where they are fighting an Islamic insurgency.
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