Higher aerobic fitness, a physiological marker of habitual physical activity, is likely to predict higher executive function based on the prefrontal cortex (PFC), according to current cross-sectional studies. The exact biological link between the brain and the brawn remains unclear, but the brain dopaminergic system, which acts as a driving force for physical activity and exercise, can be hypothesized to connect the missing link above. Recently, spontaneous eye blink rate (sEBR) was proposed and has been used as a potential, noninvasive marker of brain dopaminergic activity in the neuroscience field. To address the hypothesis above, we sought to determine whether sEBR is a mediator of the association between executive function and aerobic fitness. Thirty-five healthy young males (18-24 yr old) had their sEBR measured while staring at a fixation cross while at rest. They underwent an aerobic fitness assessment using a graded exercise test to exhaustion and performed a color-word Stroop task as an index of executive function. Stroop task-related cortical activation in the left dorsolateral PFC (l-DLPFC) was monitored using functional near-infrared spectroscopy. Correlation analyses revealed significant correlations among higher aerobic fitness, less Stroop interference, and higher sEBR. Moreover, mediation analyses showed that sEBR significantly mediated the association between aerobic fitness and Stroop interference. In addition, higher sEBR was correlated with higher neural efficiency of the l-DLPFC (i.e., executive function was high, and the corresponding l-DLPFC activation was relatively low). These results indicate that the sEBR mediates the association between aerobic fitness and executive function through prefrontal neural efficiency, which clearly supports the hypothesis that brain dopaminergic function works to connect, at least in part, the missing link between aerobic fitness and executive function.