Background This study examined associations of fitness and fatness with cognitive processes, academic achievement, and behavior, independent of demographic factors, at the baseline of an exercise trial. Methods Overweight, sedentary but otherwise healthy 7–11 year olds (N = 170) participated in a study of health, cognition and achievement in the Augusta, GA area from 2003–2006. Children underwent evaluations of fatness and fitness, psychological assessments of cognition and academic achievement, and behavior ratings by parents and teachers. Partial correlations examined associations of fitness and fatness with cognitive and achievement scores and behavior ratings, controlling for demographic factors. Results Fitness was associated with better cognition, achievement and behavior, and fatness with worse scores. Specifically, executive function, mathematics and reading achievement, and parent ratings of child behavior were related to fitness and fatness. Teacher ratings were related to fitness. Conclusion These results extend prior studies by providing reliable, standardized measures of cognitive processes, achievement, and behavior in relation to detailed measures of fitness and fatness. However, cross-sectional associations do not necessarily indicate that improving one factor, such as fatness or fitness, will result in improvements in factors that were associated with it. Thus, randomized clinical trials are necessary to determine the effects of interventions.