Purpose: To determine any associations between obesity and caries activity in the mixed dentition stage among primary school children in a low-income Mexican primary school. Materials and Methods: This cross-sectional study was performed in Mexican schoolchildren aged 8–12 years. The body mass index (BMI) was obtained, and children were classified as overweight/obese considering age and sex. The experience of caries in permanent and temporary dentition was established with the sum of decayed/missing/filled teeth (DMFT or deft index for permanent or temporal dentition); a caries index for all teeth was also considered (total decay [TD]). Mann–Whitney U-test was used to contrast the distribution between sexes of the quantitative variables and to contrast the distribution of each variable per category, the Kruskal–Wallis test was used. Spearman's Rho test was used to establish the correlation between the quantitative variables. Multiple linear regression models were performed to find the relationship between the O'Leary index and the BMI. A Multilayer Perceptron was constructed as follows: (a) dependent variables: deft, DMFT, TD and O'Leary index; (b) factor: BMI; (c) covariable: age. Results: A total of 331 children were included in the study. Dental caries prevalence was 32.4% (95% CI 29.7–35.2), while the mean DMFT was 0.64 (± SD 1.00). Through the Spearmen test, a statistically significant negative correlation was found between BMI-for-age with the total experience of carious lesions (r = –0.127, p = 0.021) and with experience of carious lesions in the deciduous dentition (deft) (r = -0.195, p ≤0.001). But when using the linear and logistic regression models to analyse the relationship with the O'Leary index, BMI was not statistically significant. With the Multilayer Perceptron there appears to be less error in the prediction of deft than the other indexes. Conclusions: This study confirms the high prevalence of obesity in primary school children. It also shows the scarce association between carious lesions and obesity.