Childhood obesity and its negative relation with children’s brain health has become a growing health concern. Over the last decade, literature has indicated that physical activity attenuates cognitive impairment associated with obesity and excess adiposity in children. However, there is no comprehensive review that considers the extent to which these factors affect different domains of cognition. This narrative review comprehensively summarizes behavioral, neuroimaging, and neuroelectric findings associated with chronic physical activity and fitness on brain and cognition in childhood obesity. Based on the literature reviewed, increased adiposity has a demonstrated relationship with neurocognitive health via mechanisms triggered by central inflammation and insulin resistance, with the most pronounced decrements observed for cognitive domains that are prefrontal- and hippocampal-dependent. Fortunately, physical activity, especially interventions enhancing aerobic fitness and motor coordination, have demonstrated efficacy for attenuating the negative effects of obesity across different subdomains of structural and functional brain imaging, cognition, and multiple academic outcomes in children with overweight or obesity. Such mitigating effects may be accounted for by attenuated central inflammation, improved insulin sensitivity, and increased expression of neurotrophic factors. Lastly, individual differences appear to play a role in this relationship, as the manipulation of physical activity characteristics, the employment of a wide array of cognitive and academic measures, the inclusion of different adiposity measures that are sensitive to neurocognitive function, and the utilization of an inter-disciplinary approach have been found to influence the relationship between physical activity and excess adiposity on brain and cognition.