Thermal comfort is an important aspect to take into consideration for the indoor environment of a building integrated with a semi-transparent Photovoltaics (STPV) system. The thermal comfort of units with photovoltaic windows and that of conventional windows, which is an ordinary without PV, were evaluated via on-site tests and questionnaires. Using the thermal comfort investigation of the test rig, the maximum difference in air temperature was found to be around 5 °C between test unit and comparison unit. The predicted mean vote (PMV)–predicted percentage dissatisfied (PPD) value of the test unit was better than that of the comparison unit. It was observed that on sunny days, the PMV value ranged from 0.2 (nature) to 1.3 (slightly warm) in the test unit, and that of the comparison unit was 0.7 (slightly warm) to 2.0 (warm), thereby providing better thermal comfort, especially during mornings. The maximum difference in PPD values was found to reach 27% between the two units at noon. On cloudy days, the difference was negligible, and the thermal sensation between the foot and the head were almost the same. Fifty respondents were asked to complete a carefully designed questionnaire. The thermal sensation of the test unit was better than that of comparison unit, which corresponded with the test results. Thermal, lighting, acoustic, and other environment comfort scores were combined, and the acceptance of the test unit with the STPV windows was found to be 73.8%. The thermal sensation difference between men and women was around 5%. Thus, during summer, STPV windows can improve the thermal comfort and potentially reduce the air-conditioning load.