This study aims to identify differences and lessons in eco-school planning techniques and sustainable design methods by analyzing comparatively green building certification system and the cases of sustainable schools in US, Korea and Japan. As a result of the comparative analysis, green building certification system for school facilities, both domestic and international, is categorized into external environment, energy, materials and resources, and indoor environment. From the case study, it is common that roof garden and biotopes are installed for external environment, while energy saving, passive energy utilization methods for natural lighting and ventilation such as arrangement planning, courtyard, top-light, shading devices, solar panel and insulation by roof garden are most frequently used. Also, storm water uses, water saving equipment and sustainable materials are often introduced for resource savings. Concerns for indoor environment is frequently addressed by introducing natural light and ventilation in the buildings, which makes ultimately a comfortable space.