The purpose of this study is to design a Wisdom-Based Leadership Model (WBLM) from an Islamic perspective for educational organizations, using qualitative approach and thematic analysis method. In order to achieve this goal, the concept of wisdom was purposefully identified based on the Quranic and narrative sources, and then WBLM was designed through thematic analysis method. In assessing the validity of the designed model, the statistical population included researchers, founders, administrators, and teachers of special schools, among whom 30 subjects were selected through purposeful sampling. Data collection tool was a valid and reliable in-depth semi-structured interview. The findings indicated that WBLM is composed of four factors (revelatory rationality, realistic empowerment, growth-oriented prevention, and timely operationalization) as well as thirteen components. Thus, WBLM can guide leaders in dealing with complex and multidimensional issues in educational settings. In this way, they can make timely decisions through targeted influence and guidance in all the epistemic and practical affairs of the educational environment, using revelatory rationality and growth-oriented preventive perspective, and consider realistic empowerment in all aspects of the educational environment.