BACKGROUND: It has been suggested that obese children have lower cognitive function, demonstrate poorer physical performance and are more susceptible to social-emotional problems. AIMS: To describe associations between human physical growth, cognitive development, physical fitness and social-emotional characteristics of obese and non-obese children and to verify the predictors of intellectual coefficient by socioeconomic status (SES). SUBJECTS AND METHODS: A sample of 107 non-obese (N-Ob) children [-1 z-score body mass index (BMI) ≤1 z-score] and 108 obese (Ob) children [2 z-score ≤BMI ≤5 z-score] from a larger cohort was evaluated. Intellectual coefficient (IQ), social-emotional wellbeing (SEW), 6-minute walk test (6MWT) and SES (mid-low, low and very low) were assessed. RESULTS: Ob children were taller, heavier and present more height for age and BMI than N-Ob children (p < 0.001). A significant correlation between IQ and SEW (r = 0.14), 6MWT and BMI z-score (r = -0.18) and 6MWT and SEW (r = 0.15) was found. Multiple regression analysis revealed that BMI z-score had a negative impact on IQ in the mid-low SES sub-group and that SEW had a positive effect on IQ in the very-low SES sub-group. CONCLUSIONS: In Chilean pre-school children from low-income families cognitive ability varied according to SES.