Students in naturally ventilated school classrooms are exposed to warmer conditions for extended periods due to intensified heat waves brought on by global warming. This study aims to investigate thermal comfort and assess the overheating risk in three secondary schools in Malaysia. Four classrooms, which consist of students aged 13 to 16 years, were selected, and the thermal environments were measured for one day at each school, simultaneously with questionnaire surveys. Indoor air temperature was found to be higher than the outdoor temperature. A comfort temperature of 29.6 °C was obtained from the Griffiths method, and when feeling a neutral sensation, students much prefer cooler environments. All classrooms exceed the overheating fixed threshold temperature of 28.0 °C at a proportion of less than 13%. Based on the adaptive overheating criteria, the overheating risk was only 2%, indicating no overheating and minimal discomfort. This study provides insight into the overheating scenario in typical school classrooms in a hothumid climate.