The indoor thermal comfort and air quality in classrooms have become of interest worldwide, predominantly because of their influence on children’s health, learning performance and productivity. Growing concerns with building energy efficiency emphasize the significance of this topic. This paper illustrates the outcome of a field study conducted in secondary school classrooms in Sydney, Australia, during the school year in 2018/2019. The procedure of the study consists of two approaches to collecting data including survey questionnaires designed for the young population, and measurements of physical variables. The study includes long-term measurements of environmental parameters in two adjacent classrooms (air temperature, relative humidity, CO2), spot measurements of indoor air quality (PM10, PM2.5, and Formaldehyde), and questionnaire surveys designed to match the students’ cognitive level. The participants were students aged between 12 and 18. The questionnaire includes questions about thermal perception, air quality and air movement, clothing level, and health condition. Surveyed classrooms used natural ventilation as the main conditioning strategy during the surveys. The infiltration and ventilation rate were studied during the non-occupied period based on the concentration decay method and a ventilation profile was created. In one of the two studied classrooms, a hybrid ventilation system was installed during autumn/mid-season 2019 to improve air quality and ventilation. This study investigates the subjective evaluation of the classroom thermal environment, which includes the analysis of children’s subjective assessment and monitoring results. The indoor air temperature reached 29 °C during mid-season and 27 °C during winter. The maximum carbon dioxide (CO2) concentrations per classroom exceeded 2900 ppm during the occupied period. The mean infiltration rate in air changes per hour (ACH) was 0.87, and ventilation rate with one window open was 2.35 ACH and reached 21.07 ACH when all windows and door were open. Improving the thermal environment and air quality is of importance in school building design, mainly because of the adverse effect of elevated temperature on children’s performance. This is an indication that new child-based design guidelines are required to improve the thermal conditions and air quality in future school buildings wherein assessments of students’ satisfaction along with energy consumption are undertaken.