Abstract Cerebral blood flow increases more during water-based exercise than land-based exercise owing to the effects of end-tidal CO 2 (PETCO 2 ) and mean arterial pressure (MAP) changes due to water immersion. However, it is unclear whether oxygenated hemoglobin (oxy-Hb) concentrations in the prefrontal cortex (PFC) are increased more by water-based or land-based exercise. We hypothesized that oxy-Hb concentrations in the PFC are higher during water-based exercise than land-based exercise when the exercise intensity is matched. To test this hypothesis, 10 healthy participants (age: 24.2 ± 1.7 years; height: 1.75 ± 0.04 m; weight: 69.5 ± 5.2 kg) performed light- to moderate-intensity cycling exercise in water (water-based cycling (WC); chest-high water at 30 °C) and on land (LC). Stroke volume, cardio output, heart rate, MAP, respiratory rate, PETCO 2 , and oxy-Hb in the PFC were assessed during 15 min of exercise, with exercise intensity increased every 5 min. Both WC and LC significantly increased oxy-Hb concentrations in the PFC as exercise intensity was increased (intensity effect: p textless 0.001). There was no significant difference in oxy-Hb concentrations during WC and LC in most prefrontal areas, although significant differences were found in areas corresponding to the left dorsolateral PFC (exercise effect: p textless 0.001). Thus, WC and LC increase oxy-Hb concentrations in the PFC in a similar manner with increasing exercise intensity, but part of the PFC exhibits enhanced oxy-Hb levels during WC. The neural response of the PFC may differ during water-based and land-based exercise owing to differences in external information associated with water immersion.