Indoor air quality (IAQ) in classrooms has a significant impact on children's academic performance, health, and well‐being; therefore, understanding children's perception of IAQ is vital. This study investigates how children's perception of IAQ is affected by environmental variables and thermal sensation. In total, 29 naturally ventilated classrooms in eight UK primary schools were selected and 805 children were surveyed during non‐heating and heating seasons. Results show that air sensation votes (ASVs) are more correlated to CO₂ levels than to operative temperatures (T_op) during non‐heating seasons and more correlated to T_op than CO₂ levels during heating seasons. The impact of T_op on ASVs decreases with an increase in CO₂ levels, and the effect of CO₂ levels on ASVs decreases with increase in T_op. The most favorable ASVs are given when children feel “cool” and have “as it is” preference. By keeping CO₂ < 1000 ppm and T_op within children's thermal comfort band, ASVs are improved by 43%. The study recommends that standards should consider the impact of both temperature and CO₂ levels on perceived IAQ. Perception of IAQ also affects children's overall comfort and tiredness levels; however, this influence is more significant on tiredness level than that on overall comfort level.