This study aimed to analyze the associations of activity‐rest pattern indicators with academic achievement, executive function, and intelligence and to explore whether these associations are mediated by the total gray matter volume among children with overweight/obesity. Ninety‐five children (10 ± 1 year, 37 girls) with overweight/obesity (based on the World Obesity Federation body mass index cutoff points) were included in this cross‐sectional study. Hip‐ and wrist‐worn ActiGraph GT3X + accelerometers were used to assess the activity‐rest pattern. Interdaily stability (IS), intradaily variability (IV), the mean value of the lowest 5 hours (L5), and the mean value of the maximum 10 hours (M10) of activity and their respective timing (TL5, TM10) were used as indicators of the activity‐rest pattern throughout the day. Chronotype and social jetlag were used as indicators of circadian preference. Academic achievement, executive function, and intelligence were assessed with standardized tests. Gray matter volume was acquired by magnetic resonance imaging (MRI). IS was positively associated with executive function (β = 0.244, P = .014). IV was negatively associated with mathematics and academic applications (β: −0.211 to −0.238, P’s ≤ .026). Later TM10 in the day was related to lower writing, academic skills, and intelligence (β: −0.229 to −0.271, P’s ≤ .025). None of the associations found were mediated by gray matter volume. A non‐fragmented and stable activity‐rest pattern and earlier physical activity in the day were associated with better academic achievement, executive function, and intelligence in children with overweight/obesity. Further studies are required to corroborate or contrast our findings.