Background: In adults, cardiovascular risk factors are known to be associated with brain health. We hypothesized that these associations are already present at school-age. We examined the associations of adverse body fat measures and cardiovascular risk factors with brain structure, including volumetric measures and white matter microstructure, in 10-year-old children. Methods: We performed a cross-sectional analysis in a population-based prospective cohort study in Rotterdam, the Netherlands. Analyses were based on 3098 children aged 10 years with neuroimaging data and at least one measurement of body fat and cardiovascular risk factors. Body fat measures included body mass index (BMI), fat mass index and android fat mass percentage obtained by Dual-energy X-ray absorptiometry. Cardiovascular risk factors included blood pressure, and serum glucose, insulin and lipids blood concentrations. Structural neuroimaging, including global and regional brain volumes, was quantified by magnetic resonance imaging. DTI was used to assess white matter microstructure, including global fractional anisotropy (FA) and mean diffusivity (MD). Results: As compared to children with a normal weight, those with underweight had a smaller total brain and white matter volumes (differences −18.10 (95% Confidence Interval (CI) −30.97,−5.22) cm3, −10.64 (95% CI −16.82,−4.47) cm3, respectively). In contrast, one SDS (Standard Deviation Score) increase in fat mass index was associated with a smaller gray matter volume (differences −3.48 (95% CI −16.82, −4.47) cm3). Also, one SDS increase in android fat mass percentage was associated with lower white matter diffusivity (difference −0.06 (95% CI −0.10, −0.02) SDS). None of the other cardiovascular risk factors were associated with any of the brain outcomes. Conclusions: Body fat measures, but not other cardiovascular risk factors, were associated with structural neuroimaging outcomes in school-aged children. Prospective studies are needed to assess causality, direction and long-term consequences of the associations.