Physical exercise plays a crucial role in the development of cognition and brain functions in children. Inhibitory control is an advanced cognition that affects children’s life and learning. In the current study, the relationship between physical training and inhibitory control was explored. In total, 80 children were randomly but equally assigned to the experimental and control groups. The experimental group underwent physical training (volleyball) for 60 min, thrice a week for 12 weeks. In contrast, the control group did not undergo any training and continued with their daily routines. The flanker task and functional near-infrared spectroscopy (fNIRS) were employed to investigate the effects of 12-week physical training on inhibitory control and changes in the oxy-Hb concentration in the prefrontal cortex (PFC) during the task. The behavioral results revealed that the experimental group performed better on the flanker task (e.g., shorter response time [F (1,74) = 18.420, p textless 0.001, ηp2 = 0.199] and higher accuracy [F (1,74) = 15.00, p textless 0.001, ηp2 = 0.169] than the control group. The oxy-Hb concentration in the right dorsolateral PFC (R-DLPFC) was higher and the activation level of this region was higher during the flanker task [F (1,74) = 6.216, p textless 0.05, ηp2 = 0.077]. Moreover, the McNemar test revealed improved cognitive performance in response time or accuracy and R-DLPFC activation induced by physical exercise coincided significantly (χ2 = 5.49, p textless 0.05; χ2 = 6.081, p textless 0.05). These findings suggest that the R-DLPFC is likely the neural substrate for improved cognitive performance elicited by 12-week physical training.