The current study examined the effects of acute moderate-intensity aerobic exercise (MAE) on inhibitory control and resting-state heart rate variability (HRV) in children with Attention-Deficit/Hyperactivity Disorder (ADHD). Our data show that acute MAE resulted in higher response accuracy of a modified flanker task regardless of task difficulty for 60 min (p = .001). Aerobic exercise further resulted in more effective conflict detection, as measured by greater amplitude (p = .012) and shorter latency (p = .029) of the N2 component of event-related brain potential, for 60 min regardless of task difficulty. In contrast, acute MAE did not modulate sympathovagal balance signified by HRV at either 30 min or 60 min following exercise cessation. Collectively, our findings suggest that the beneficial effects of acute aerobic exercise on inhibitory control are sustained for 60 min in children with ADHD. However, acute aerobic exercise may not modulate sympathovagal balance during the post-exercise recovery. Overall, we highlight the importance of acute aerobic exercise for children with ADHD as a potential means to facilitate brain health.