The paper analyzes the theoretical and methodological basis of the organization of management of educational institutions, especially in the organization of management of educational institutions with inclusive education based on innovative technologies. Lack of conceptual and operational-practical aspects of management of educational institutions, which leads to spontaneity in the mechanisms of innovation management, lack of definition of target and value aspects of such changes, necessitates the development of a new model of management of educational institutions that would take into account new trends in inclusive education, provided favorable conditions for innovation, asserted humanistic values as a priority in the development of innovative educational space. The paper presents and scientifically substantiates the model of management of educational institutions with inclusive education based on innovative technologies, as well as key components of the organization of the educational process, which determine the areas of management in educational institutions. The algorithm of the introduction of managerial innovative technologies is offered, and also the innovative technologies which are necessary for the realization of the model of innovative management of educational institutions with inclusive training are systematized and analyzed. Analyzing the results of the experiment, it can be argued that innovative technologies are a necessary condition for successful innovation management. The introduction of innovative educational management requires an analysis of all stages of innovation, from the process of preparation to the introduction of innovations; finding out the direction of pedagogical processes, trends in their development, compliance with goals, identifying potential opportunities for the system.