It has been reported that there is a large issue regarding the IEQ in schools and classrooms as they often do not have a mechanical ventilation system or do not operate it to save on electricity bills. However, the measurements and reports from existing research indicate that the indoor air temperatures and CO2 levels are often way outside the recommended values and manual venting by opening windows during brakes is not sufficient. This has become especially alarming during the COVID-19 pandemic, as the virus can spread through the air and under-ventilated classrooms pose a great risk for the pupils located in them. In the scope of this paper, a classroom was simulated concerning IAQ and thermal comfort at various ventilation strategies. The simulation was used to determine the predicted thermal comfort at various locations in the classroom at different window opening areas and orientations. Based on the simulation results potential control strategies for window ventilation were developed. They take into account the changing location of persons and the threshold level of allowed deviation from optimal thermal comfort level to achieve the optimal IAQ as a compromise during the cold winter periods must be made. The results indicated that after 50-second-long natural ventilation at an outside air temperature of -3 °C the thermal comfort level will be very low in most of the points of the classroom. None of the various window-opening strategies influences this much. The lowest achieved average PPD was 62.5% and it was in the case when one open window was open at 90 but in the case when two windows were open at 15 cm the average PPD was 98.7%.