In the present research work, the thermal comfort of an educational building in a semi-arid climate of Lahore, Pakistan has been analyzed based on the PMV-PPD method using a subjective scale in terms of acceptability, neutrality, and preference, considering the impact of gender. Firstly, this study examine how the temperature affects occupants\' (male and female) comfort levels in current university classrooms during the winter and summer. Secondly, how occupant behavior affects thermal comfort, productivity, and health well-being to determine how future buildings should be designed to accommodate gender preferences. Thirdly, the study improve retrofitting approaches for building systems that make it satisfies inhabitants\' thermal requirements, and is cost and energy effective. This study revealed that females were more affected by winter conditions while males were more affected by higher temperatures in summers. In both seasons, males found a frequent impact of thermal comfort, due to which more productivity loss was observed in them in comparison to females. In winter, females were more affected form SBS, and in summer, males showed more symptoms of getting affected by SBS. The overall percentage saving in energy consumption was found 27 % for considered Building compared with retrofitted simulated model of building systems. It is suggested that a well-insulated indoor thermal environment is the need of the hour for classrooms in university buildings to improve the thermal comfort conditions, productivity and health conditions of the occupants for both seasons.