Exercise is an integral part of children's lives, and research in educational settings has found that regular engagement promises improvements in executive function (i.e. top-down control of goal-directed behavior). Based on recent advances in understanding the moderators and the neurocognitive mechanisms of these effects, we highlight a potential application of exercise in the treatment of executive dysfunction. Even though different neurodevelopmental disorders are characterized by a heterogeneity in core symptoms, children affected by these disorders often face common executive function deficits. So far, exercise has not been recognized as an alternative or additional treatment for this specific cognitive impairment. The limited experimental evidence in children with neurodevelopmental disorders provides a first indication that regular exercise engagement benefits executive function. However, we identified key research questions that need to be answered before a prescription of exercise to children with executive dysfunction can be encouraged in clinical practice.