Contemporary school should create favorable conditions for schoolchildren. The aim of the study was to comparatively analyze risk factors related to the educational process in different schools and to develop a new approach to objective assessment of combined exposure to environmental factors and factors related to the educational process and its influence on schoolchildren’s health. The study focused on the following research objects: 1) five different secondary schools, the test ones providing profound educational programs and the reference ones being ordinary secondary schools with the same or lower levels of pollution in environmental objects; 2) quality of components in the school environment (organization of the educational process, quality of meals provided by school, quality of ambient air on a school territory and inside a school, quality of drinking water, socioeconomic conditions); 3) health of 756 schoolchildren. The study was conducted by using sanitary-epidemiological, sanitary-hygienic and sociological methods; clinical and laboratory examinations; chemical analytical tests. Fuzzy logic was applied to estimate combined influence exerted by factors related to the educational process and environmental factors. We established several determinants of negative effects produced by the educational process on schoolchildren’s health. They included elevated intensity and monotony of educational and intellectual loads, shorter breaks between classes and recovery index deficiency. Diet-related factors included excess consumption of fats and carbohydrates, overall caloric contents being too high, protein and micronutrient deficiency. Chemical factors were elevated levels of metals, aromatic hydrocarbons, aldehydes, and chlorinated organic compounds in biological media. Risk-inducing factors of schoolchildren, regardless of a school and age, include organization of the educational process (Ipj = 0.45–0.58) and school meals (Ipj = 0.41–0.54); the group potential hazard index for these factors reached its peak values in primary school (Ipj = 0.49–0.58 and Ipj = 0.46–0.54). The maximum value of the integral potential hazard index (Ipdk = 0.41–0.46) caused by combined exposure to factors related to the educational process and environmental factors, regardless of a school type, was detected in senior schoolchildren in school with profound studies of natural sciences (Ipdk = 0.41); the minimum value was detected in a military school (Ipdk = 0.33).