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When studying the theoretical foundations of the transformation of the management system of an educational organization, the management system is understood as scientifically based actions on the part of the administration and the teaching staff of the organization, which are aimed at the rational use of available forces, time and material resources, in order to implement an effective pedagogical process within a specific educational organization. As practice shows, most educational organizations are characterized by a linear-functional organizational structure, as a result of which the management system is not mobile, it does not allow taking into account the peculiarities of the human capital of the teaching staff, weakly forms the interest of each member of the team in the final result. The article considers one of the most effective management tools in conditions when an educational organization faces the task of increasing its efficiency and effectiveness with limited resources – project management. Its implementation in the conditions of digitalization will allow educational organizations to carry out more effective strategic interaction, due to the formation of a network contact. The aim of the study is to improve the management system in a secondary school. To solve the tasks set in the work, the following research methods are used: theoretical methods – analysis and generalization of pedagogical, managerial, methodological and scientific-theoretical literature; normative documents regulating the management of an educational organization; teaching aids on the following aspects: management system, digital transformation of education, management of an educational organization, project management. In the course of our work, we came to the conclusion that the process of managing an educational organization in modern times is prone to a trend that manifests itself in a widespread, global transformation of the management system of an educational organization. One of the features of the management of the educational system is the departure from traditional forms of organizational structure, the restructuring of structures in accordance with the requirements of high efficiency in solving issues, the creation of conditions for participation in decision-making by all members of the workforce. Thus, project management is one of the most effective management tools in conditions when an educational organization faces the task of increasing its efficiency and effectiveness with limited resources.