Several neuroimaging studies have examined the effect of different types and combinations of exercises on activation of brain associated with cognitive testing but none of these studies have examined the role of high intensity intermittent exercise (HIIE) in altering cortical activation from simple to complex cognitive tasks. The purpose of this study was to find if HIIE has a role in modulating executive functions related to inhibitory control as expressed by changes in prefrontal cortex (PFC) activation. Materials and methods. 40 healthy adults aged between 18-30 years volunteered for the study. They were randomly divided into HIIE a (n = 20) group and a control (n = 20) group. The HIIE group performed 4*4 min of high intensity exercise on a cycle ergometer with 3 minutes of active recovery at lower intensities between the bouts, whereas the control group performed no exercise. Prefrontal hemodynamics (oxy and deoxy haemoglobin) were assessed using functional near infrared spectroscopy (fNIRS) during the Colour Word Stroop test (CWST) on two sessions: pre-session and post-session (1 week after pre-session). Results. The results indicate a significant difference in CWST scores which coincided with a significant difference in hemodynamics of PFC between a congruent and a complex incongruent task in the HIIE group. There was a greater activation of the right frontopolar area, the left ventrolateral prefrontal cortex, and the left frontopolar area during the incongruent task in response to acute HIIE. Conclusion. HIIE plays a role in changing brain activation during more complex interference related tasks.