This document presents the natural ventilation operational guide for educational buildings developed by the IAQ4EDU project. Most educational buildings are completely naturally ventilated. This challenges the indoor environmental quality management of schools in terms of balancing the needs of students for indoor air quality and thermal comfort. This guide presents the conditions and methods of using natural ventilation strategies to maintain good air quality and thermal comfort in classrooms. Using the example of Catalonia (Spain), a general ventilation protocol was developed to guide teachers in implementing natural ventilation in different seasons to ensure air quality during school hours. Relevant users can refer to the case in this practical guide to develop ventilation protocols based on the local climate and school conditions.