Running, compared to pedaling is a whole-body locomotive movement that may confer more mental health via strongly stimulating brains, although running impacts on mental health but their underlying brain mechanisms have yet to be determined; since almost the mechanistic studies have been done with pedaling. We thus aimed at determining the acute effect of a single bout of running at moderate-intensity, the most popular condition, on mood and executive function as well as their neural substrates in the prefrontal cortex (PFC). Twenty-six healthy participants completed both a 10-min running session on a treadmill at 50%[Formula: see text] and a resting control session in randomized order. Executive function was assessed using the Stroop interference time from the color-word matching Stroop task (CWST) and mood was assessed using the Two-Dimensional Mood Scale, before and after both sessions. Prefrontal hemodynamic changes while performing the CWST were investigated using functional near-infrared spectroscopy. Running resulted in significant enhanced arousal and pleasure level compared to control. Running also caused significant greater reduction of Stroop interference time and increase in Oxy-Hb signals in bilateral PFCs. Besides, we found a significant association among pleasure level, Stroop interference reaction time, and the left dorsolateral PFCs: important brain loci for inhibitory control and mood regulation. To our knowledge, an acute moderate-intensity running has the beneficial of inducing a positive mood and enhancing executive function coinciding with cortical activation in the prefrontal subregions involved in inhibitory control and mood regulation. These results together with previous findings with pedaling imply the specificity of moderate running benefits promoting both cognition and pleasant mood.