The high prevalence of nutrition-related disorders among children necessitates the development of new methods for assessing the effects of nutrition on the body. Heart rate variability (HRV) analysis combined with the body mass index (BMI) calculation constitute an effective non-invasive health status assessment protocol. This cross-sectional study aimed to evaluate the dietary patterns of schoolchildren in Yekaterinburg and examine their associations with BMI and indicators of autonomic nervous system function. We recruited 202 schoolchildren aged 11−12 years; their diets were assessed using the frequency method and by calculating the nutrition quality index (NQI). We collected the participants' anthropometric data, measured their bioimpedance, and analyzed the HRV. Nonparametric methods, odds ratio calculation (ORC) and cluster analysis were used for statistical processing. It was found that the quality of the diets of 67.3% of schoolchildren was unsatisfactory: their diets were excessive in saturated fats, added sugars, and sodium, and deficient in dietary fiber, complete proteins, B vitamins, vitamin A, calcium, and magnesium. Children with a low NQI are 5.5 times more likely to be overweight and have a higher body-fat percentage than their peers with a satisfactory diet. HRV indicators differed significantly according to dietary patterns: children who consumed large amounts of vegetables and fruit exhibited more favorable heart rate variability, whereas those whose diets were high in added sugars and fats had the least favorable HRV. The identified abnormalities highlight the need to develop preventive programs aimed at improving eating habits and to consider introducing HRV monitoring into the schoolchildren's health hygienic assessment system.