The mainly Buddhist men and women now have one of the deadliest jobs in the country and say bringing a gun to school has become essential.
Sanguan Jintarat, head of the Teachers' Association that oversees 15,000 teachers in the south, said: "You'd never see a teacher elsewhere in Thailand carrying a gun. But we need them, or we'll die."
Officials say teachers may be targets because they are symbols of the central government's authority, or be taken hostage to be traded for captured insurgents.
Militants may also want to do away with secular schools, sending the message that only Islamic schools - which have been spared violence - are safe.
More than 1,700 people have been killed across Yala, Pattani and Narathiwat, the only Muslim-majority province. They include 44 teachers.
Among them was a teacher gunned down at his blackboard as he taught and a Buddhist art teacher clubbed by a village mob until her skull shattered.
A study by Srisompob Jitipirmosri, a political science professor at Prince of Songkhla university in Pattani province, shows that nearly 300 schools and teachers have been targeted - mostly arson, bomb attacks and shooting at guarded teacher convoys going to and from school.
Strict gun laws have been relaxed for teachers, who are eligible for a special permit to carry weapons in the three provinces. But bureaucracy and high demand delay the processing of applications by months.
Thousands of teachers and principals carry guns - many without permits - and hundreds are waiting for training. Around 100 state school teachers recently underwent weapons training at the Chulabhorn naval base on the Gulf of Thailand. They included Aree Aatomphrasangsa, a 50-year-old elementary school principal, who says she owns two shotguns. Her school is in the Sisakorn district of Narathiwat province, in an area dubbed the "Red Zone" - a classification reserved for the most dangerous districts.
"I want a small gun, a revolver," said slight, bespectacled woman as she walked off the military shooting range with a tray of blanks. A revolver is easy to carry and shoot. When I drive, I can hold the steering wheel with one hand and use the other hand to shoot."