SummaryBackgroundChildren with obesity show differences in brain structure, executive function and appetitive traits when compared with lean peers. Little is known on the relationship between brain structure and these traits.ObjectivesTo investigate the relationship between differences in brain structure and executive function and appetitive traits, in obese and lean adolescents.MethodsMRI was used to measure cortical thickness and subcortical volumes. Executive function was measured by a Stop Signal‐and a Choice Delay Task. Appetitive traits were measured using the Child Eating Behaviour Questionnaire.ResultsAdolescents with obesity had greater volumes of the pallidum; 1.78 mL (SE 0.03, p=0.014), when compared with controls; 1.65 mL (SE 0.02). In the group with obesity, greater pallidum volume was positively associated with the ability to delay reward in the Choice Delay Task (p=0.012).ConclusionThe association between pallidum volumes and Choice Delay Task in obese adolescents supports the hypothesis that the pallidum plays an important role in executive dysfunction in obese children.