Background <p>The flow phenomenon, achieving a heightened state of concentration, is characterized by an autotelic experience, which may reduce the perception of physical exertion during sports activities. It has been extensively documented in sports and is associated with exceptional performance. However, despite comprehensive descriptions of the autotelic experience in flow, the physiological mechanisms underlying flow remain elusive, limiting its reproducibility and broader application. This study aimed to elucidate the contribution of flow to the discrepancies between perceived exercise intensity and physiological intensity during endurance exercise using an exercise bike.</p> Methods <p>We assessed specific conditions conducive to flow during endurance exercise on a bicycle ergometer. Flow states were evaluated using a shortened version of the Flow State Scale, whereas subjective perceptions of exercise intensity were measured using the Rating of Perceived Exertion (RPE). Physiological responses were monitored by measuring heart rate (HR), oxygen consumption, breathing frequency, ventilation, and oxy- and deoxy-hemoglobin levels for changes in cerebral oxygenation at the prefrontal cortex assessed using near-infrared spectroscopy.</p> Results <p>Participants were categorized into RPE alleviation and escalation groups to examine individual differences in perceived exertion. RPE changes significantly differed between the two groups (<i>p</i> = 0.0002), despite no significant difference in HR changes (<i>p</i> = 0.36). The discrepancy ratios between perceived and physiological exercise intensity also significantly differed between groups (<i>p</i> = 0.001) and were negatively correlated with flow state levels (<i>r</i> = − 0.56).</p> Conclusions <p>These findings advance our understanding of the physiological and neurological correlates of flow states during physical activity, with potential applications extending beyond sports performance enhancement to domains such as education and arts.</p>