Objective of the study was to scientifically substantiate the innovative-synergistic method of educational process management in physical culture university. Methods and structure of the study. When organizing and running the experiments (educational - natural, economic - at the micro-level - "scientific organization of labor, production and management"), the following stages were distinguished: theoretical (definition of the problem, definition of the goal, object, and subject of the research, its tasks and hypotheses); methodological (development of the research methodology, its plan, program, methods of processing of the data obtained); actual experiment - a series of tests (creation of experimental situations, observation, experience management); analytical - quantitative and qualitative analysis, interpretation of the received facts, drawing conclusions and elaborating practical recommendations. Study results and conclusions. The article covers the issues of innovative (electronic) management of the educational institutions. We theoretically substantiated the necessity and looked into the managerial measures to introduce into the process of management of the physical education and sports institutions a unified electronic rating system for assessment of students' knowledge and staff expertise level as required by the professional standard and academic curriculum of this program, the didactic basis of which is the innovative-synergetic management system that causes changes not only within the range allowed by the homeostatic functions but also through the processes of self-organization in the educational environment of the educational institution.