This review examines the impact of school building design on indoor air quality (IAQ) and thermal comfort, focusing on the role of the building’s energy performance and natural ventilation in ensuring good and stable indoor conditions. Educational facilities often face indoor comfort challenges due to high occupancy levels, outdated technologies, and limited maintenance budgets. The design of a school building is very important and is the first step in achieving good indoor environmental conditions. Starting from the orientation of the building, its shape, architectural and technological characteristics, the building is responsible for whether it can improve the IAQ and guarantee the right comfort. School building renovation measures to improve energy performance and indoor micro-climate conditions include those involving the HVAC system and those acting on the building envelope, improving its performance, airtightness and thermal insulation. Among the passive strategies, passive retrofit solutions such as thermal masses and night ventilation have proven to be particularly effective in ensuring a good balance between air quality, thermal comfort and energy consumption. The review also addresses the complexities of maintaining good IAQ in schools and offers insights into sustainable design practices that balance comfort, air quality, and energy efficiency.