It is well-established that cognitive functions are an important factor that affects children’s learning. Children with Attention-Deficit/Hyperactivity Disorder (ADHD), however, often suffer from learning difficulties and social adaptation problems due to their lack of sustained attention and inhibitory control. While research has shown that acute exercise can improve cognitive functions, the duration of such beneficial effects is yet to be confirmed. Moreover, objective benchmarks such as event-related brain potentials (ERP) and resting-state heart rate variability (HRV) are less used in physical and psychological observation. The objective of this study was to understand the sustained effects of acute moderate-intensity aerobic exercise (MAE) on inhibitory control in children with ADHD. A within-subject design was conducted on 24 children diagnosed with ADHD ranging from 8-12 years old, and the changes in inhibitory control, heart rate variability (HRV), and event-related potentials (ERP) indices were observed within one hour after an exercise intervention condition or a control condition. The results indicated that acute bouts of MAE facilitate inhibitory control in children with ADHD for as long as 60 min, which was reflected in the children’s performance and ERP measurements. 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.