Leadership has an important role in the educational institutions. The increasing number of implementation models of integrative Islamic education institutions demand greater competence of the leaders in order to perform their duties effectively. The most complex integrative Islamic educational institution model is developed based on boarding school by integrating formal and nonformal education as well as cross ladder as developed by Al Mukmin Islamic Boarding School (PPIM) Ngruki and modern boarding schools in general. The result of this study shows that the effective leadership model of an integrative Islamic educational institution is a democratic-transformational model. This model needs the institutional leaders to have professional, personal, social, and spiritual competences. The integration of the educational institutions management should be done thoroughly starting from the integration of curriculum management, human resources, infrastructure, financing, public relations and marketing, and other aspects.