The objective of this study was to investigate the association of different cognitive abilities with children's body weight adjusted for further weight influencing sociodemographic, family, and lifestyle factors. Cross-sectional data of 498 primary school children (7.0 ± 0.6 years; 49.8% boys) participating in a health promotion programme in southwest Germany were used. Children performed a computer-based test battery (KiTAP) including an inhibitory control task (Go-Nogo paradigm), a cognitive flexibility task, and a sustained attention task. Height and weight were measured in a standardized manner and converted to BMI percentiles based on national standards. Sociodemographic features (migration background and parental education), family characteristics (parental body weight), and children's lifestyle (TV consumption, physical activity, consumption of sugar-sweetened beverages and breakfast habits) were assessed via parental questionnaire. A hierarchical regression analysis revealed inhibitory control and cognitive flexibility to be significant cognitive predictors for children's body weight. There was no association concerning sustained attention. The findings suggest that especially cognitive abilities known as executive functions (inhibitory control and cognitive flexibility) are associated with children's body weight. Future longitudinal and intervention studies are necessary to investigate the directionality of the association and the potential of integrating cognitive training in obesity prevention strategies. This trial is registered with ClinicalTrials.gov DRKS00000494.