Students require a comfortable thermal environment for better academic learning and health in general. In Nepal, the majority of school buildings are constructed using local materials, but little consideration is provided to the thermal environment required for comfort. Therefore, this study demonstrates the advantages of using passive design measures through a simulation that can be used either in the early stages or as a retrofit to determine how the building performs in terms of comfort and the thermal environment. First, the thermal environment of school buildings and thermal comfort of students were evaluated through field surveys. Subsequently, a simulation was performed to investigate the operative temperatures in the classroom of a school building in Kathmandu. DesignBuilder software was used to create the base model and the simulated operative temperature was validated using the measured globe temperature. Subsequently, passive strategies, such as natural ventilation, insulation, and thermal mass, were applied and analysed. The field survey showed that the indoor globe and outdoor air temperatures were correlated, and the students perceived a hotter environment and preferred a cooler environment. Within this context, the average comfort temperature was 26.9 °C. The simulation results showed that the operative temperature was reduced to below 27 °C with a maximum reduction of 3.3 °C due to the integrated design impact, which is within the comfortable limit required during school hours. This study helps to design Nepalese school buildings in a better way by considering passive design strategies during architectural design to make classrooms more thermally comfortable.