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The role of the cerebrovascular system in migraine pathogenesis is critical. Several studies have demonstrated alterations in the regional cerebral blood flow that persist during headache-free intervals. In the present study, we aimed to measure the prefrontal hemodynamic responses to the cognitive task in interictal episodic migraineurs. We enrolled eight migraine patients with aura (mean age 25.75 ± 4.39 years), twelve migraine patients without aura (mean age 28.25 ± 6.59 years), and eleven age- and education-matched healthy subjects. We employed the Victoria Stroop task to assess executive functions, specifically selective attention and inhibitory control. The mean changes in the oxy-Hb, deoxy-Hb and total Hb concentrations during the Stroop interference (incongruent minus neutral) were recorded by functional near-infrared spectroscopy (fNIRS). Our preliminary results indicated that migraine patients with aura had higher reaction time (p = 0.033) and lower prefrontal oxy-Hb activity (p = 0.036) during the Stroop interference compared to healthy subjects. For the left lateral prefrontal cortex, migraine with aura group showed lower oxy-Hb activity than the healthy subjects during the Stroop interference (p = 0.009). However, there were no such differences in the right lateral prefrontal cortex. Additionally we found a relationship between prefrontal oxygenation and the severity of headaches, the frequency of attacks, and the number of monthly migraine days. We noticed a decrease in prefrontal blood flow in migraine patients with aura, even during the interictal periods. This may indicate that migraine with aura could be a persistent neurovascular uncoupling disorder. Moreover, the reduced oxygen supply to the prefrontal cortex may be associated with impaired frontal lobe functions.