This study examined the association between obesity and deprivation in English children and whether cardiorespiratory fitness or physical activity (PA) can explain this association. Obesity was assessed using IOTF criteria in 8,398 10-16 year olds. Social deprivation was measured using the Index of Multiple Deprivation (IMD) (subdivided into 3 groups; high, mid and low deprivation). Obesity was analysed using binary logistic regression with stature, age and sex incorporated as confounding variables. Children's fitness levels were assessed using predicted VO2 max (20-metre shuttle run test) and PA was estimated using the PA Questionnaire for Adolescents or Children (PAQ). A strong association was found between obesity and deprivation. When fitness and PA were added to the logistic regression models, increasing levels in both were found to reduce the odds of obesity, although it was only by including fitness into the model that the association between obesity and deprivation disappeared. Including estimated PA into the model was found to be curvilinear. Initial increases in PA increase the odds of obesity. Only by increasing PA to exceed the 71st percentile (PAQ = 3.22) did the odds of being obese start to decline. In order to reduce deprivation inequalities in children's weight-status, health practitioners should focus on increasing cardiorespiratory fitness via physical activity levels in areas of greater deprivation.