In school buildings, indoor thermal conditions are significant, considering the academic performance of the students. Thus, this study aims to evaluate and improve thermal comfort and productivity of occupants while analyzing its effect on energy consumption in a multipurpose school building. The building represents both the workplaces (offices), learning spaces (lecture halls, seminar rooms), and leisure areas (halls, canteens). Each thermal zone was evaluated separately based on the actual conditions. Interactions between environmental conditions, control strategies and annual heating/cooling loads have been analyzed through dynamic building modeling, using DesignBuilder and EnergyPlus software. The thermal comfort of the building has been evaluated concerning the actual conditions based on Fanger's PMV index, and the results are compared with the site measurements done. The verified model was used to examine the effect of ambient temperature, supply airflow, HVAC and shading element operational schedule on thermal comfort and occupant productivity. As a result, discomfort hours were reduced by 17.6%, while it also led to an increase in annual energy consumption by 11.7%. When the change in productivity is analyzed, typing and thinking productivity were increased by 46%. The results showed that the building shell and design specifications of each zone should be considered when developing HVAC operational and design strategies to ensure better thermal comfort and productivity.