According to the adopted Federal Law No. 273-FZ of December 29, 2012 (as amended on June 27, 2013) “On Education in the Russian Federation”, preschool education is the first level of the educational process. Precisely in a preschool children, for the first time, ideas about the surrounding world are formed, a system of values, as well as knowledge and skills, that can only be corrected but not radically changed. Numerous studies have shown that, thanks to investments in the early development of man, tremendous results can be obtained in the future through the formation of national human capital, which is the basis of the country’s innovative development. However, in modern theory and practice of management in the field of education, there is no universal mechanism responsible for assessing the effectiveness and efficiency of management. Questions about the criteria, methods, indicators of this assessment and, as a result, the problem of improving the methodology for managing human capital have not been resolved. The article provides an analysis of the state of affairs in the management of the activities of preschool educational institutions and gives recommendations on improving innovative management activities in the field of preschool education, as well as a three-phase methodology of estimation of the effectiveness and efficiency of preschool education in the interests of Russia’s innovative development with appropriate approbation of the results.