Protection of health of children is the most important task before the country; preservation and strengthening of health of schoolchildren necessitates introduction of scientifically sound technologies and new methods of hygienic education. This study aimed to evaluate the effectiveness of the developed original educational program for primary schoolchildren designed to give them knowledge about rational nutrition and healthy lifestyle. From 2019 to 2020, we tested the rational nutrition and healthy lifestyle skills development program that relies on the Children and Adolescents Individual Diet Calculation and Hygienic Assessment Module. The study involved 336 schoolchildren (176 schoolchildren in the treatment group, 160 in the control group) from 4 classes of three educational institutions in Smolensk. The analysis of effectiveness of preventive measures showed that the proportion of children whose daily diet included vegetables and fruits has grown 1.5 times, and the consumption of fast food products and sugary carbonated drinks has dropped 4 and 2.5 times, respectively. Control group, where no preventive measures were implemented, exhibited no positive trends. The effectiveness of the program was confirmed by a significant decrease in the share of overweight primary schoolchildren: from 17.6% to 9.3% (2 = 5.239, p = 0.023). The results of this study allow recommending the developed nutrition and healthy lifestyle skills development program as an effective hygienic education technology for primary schoolchildren.