Introduction: Inadequate physical activity, eating disorders, irrational factors of the educational environment and a poor motivation for a healthy lifestyle are often observed among youngsters and act as their health risk factors. At the present stage, they hamper ensuring optimal living conditions and achieving better health of schoolchildren and require a new approach to solving the tasks. The objective of the study was to assess provision of sanitary and epidemiologic wellbeing at schools and health of schoolchildren to substantiate priorities for management decision making. Materials and methods: The study was conducted in two comprehensive schools of the city of Penza and involved 2,672 children and 720 parents. We used sanitary, hygienic, physiological, sociological, and statistical methods of research. Results: The level of sanitary and epidemiologic wellbeing in the experimental school with an up-to-date model of hygienic education and development of a healthy lifestyle integrated in the educational process where students have the opportunity to receive health-improving and rehabilitation medical care, was significantly higher than in the control one. Introduction of the new model of upbringing and functioning of the department for disease prevention and rehabilitation contributed to an increase in students’ motivation for a healthy lifestyle and skill consolidation in the behavior of youngsters as confirmed by a larger proportion of such students in the experimental school compared with the control one (75–89% against 50–74%, respectively; p < 0.001). Conclusion: Implementation of management decisions including the upgrade of the system of hygiene education, creation of a healthy lifestyle of students, and organization of the department for disease prevention and rehabilitation on the basis of the educational establishment had a positive effect on students’ health.