The COVID-19 pandemic began to spread at the beginning of 2020 in the world and in Japan, which is expected to impact the air conditioning (AC) energy use (EU) in educational buildings when AC and natural ventilation are used together as a new regulation to decrease infectious disease transmission. Furthermore, this regulation of natural ventilation is expected to impact the AC EU when the outside temperature affects indoor comfort causing changes in the regular AC setting temperature and AC operating times. This study aims to evaluate the AC EU, and the indoor thermal environment changes with Private Finance Initiative (PFI) data monitoring in junior high schools in Oita City before and during the COVID-19 pandemic during summer and winter through a sensitivity analysis method. The result found that AC EU significantly increased during the pandemic, 2 times escalation in summer and 1.9 times in winter. Besides, during the pandemic, indoor air temperature comfort was achieved with longer AC operation time, lower AC setting temperature in summer, and higher AC setting temperature in winter. The result of this research can be expected to be beneficial for future studies regarding AC energy saving and indoor thermal comfort-related investigation and valuable for new regulations related to air conditioner settings and operations for the new normal during the pandemic.