This article investigates a methodology for the application of the design of sunlighting and shading systems in educational settings, focusing on their impact on thermal comfort. As educational environments increasingly recognize the importance of physical comfort in enhancing learning outcomes, this study starts with an analysis of current shading practices and their effectiveness. A user-friendly methodology for assessing sunlight and shading in schools is developed, utilizing a transdisciplinary research approach, with various stakeholders, including educators, architects, and environmental scientists. Through case studies conducted in Zornotza, Spain, the research warns about the detrimental effects of inadequate shading on student well-being and proposes design solutions for each of the cases. Our findings underscore the necessity for innovative design strategies that integrate both passive and active shading solutions, ultimately contributing to healthier, more sustainable learning environments. These innovative strategies can be better oriented at the early stages of the analysis of the problem if transdisciplinary research is applied, advocating for a holistic approach to educational facility design that prioritizes the comfort and success of students.