Consequences of obesity for mental health and cognitive development are not established to the same degree as those for chronic diseases. This study aims to document the interrelationships between body weight, self-esteem and school performance in childhood. Height and weight measurements and self-report of self-esteem, diet quality and physical activity of 4945 grade 5 students were linked with standardized literacy test results. Structural equation models were applied to confirm hypothesized relationships between body weight, self-esteem and school performance, and revealed that body weight affected self-esteem negatively and that school performance affected self-esteem positively. Body weight did not affect school performance, and self-esteem did affect neither body weight nor school performance. Subsequent multi-level logistic regression showed that obese students, relative to normal weight students, were more likely (1.44; 95% CI: 1.12–1.84), and students with good school performance, relative to those performing poor, were less likely (0.39; 95% CI: 0.26–0.58), to have low self-esteem. Diet quality and active living had positive effects on both school performance and self-esteem. The study findings further establish obesity as a risk factor for low self-esteem and add to the rationale to promote healthy eating and active living among children and youth as this will prevent chronic diseases and improve mental health and cognitive development.