The acute-exercise effects upon cognitive functions are varied and dependent upon exercise duration and intensity, and the type of cognitive tasks assessed. The hypofrontality hypothesis assumes that prolonged exercise, at physiologically challenging intensities, is detrimental to executive functions due to cerebral perturbations (indicated by reduced prefrontal activity). The present study aimed to test this hypothesis by measuring oxygenation in prefrontal and motor regions using near-infrared spectroscopy during two executive tasks (flanker task and 2-back task) performed while cycling for 60 min at a very low intensity and an intensity above the ventilatory threshold. Findings revealed that, compared to very low intensity, physiologically challenging exercise (i) shortened reaction time in the flanker task, (ii) impaired performance in the 2-back task, and (iii) initially increased oxygenation in prefrontal, but not motor regions, which then became stable in both regions over time. Therefore, during prolonged exercise, not only is the intensity of exercise assessed important, but also the nature of the cognitive processes involved in the task. In contrast to the hypofrontality hypothesis, no inverse pattern of oxygenation between prefrontal and motor regions was observed, and prefrontal oxygenation was maintained over time. The present results go against the hypofrontality hypothesis.