We investigated prefrontal cortex (PFC) hemodynamic response, through functional near infrared spectroscopy (fNIRS) during executive function (EF) processing in response to acute high intensity intermittent exercise (HIIE) in young adults. We also assessed the associated sex differences in the cognitive scores and related PFC hemodynamic functions in response to HIIE. 49 young healthy adult participants (32 women, 17 men) were randomly assigned to either control or HIIE intervention groups. HIIE group participants performed 4 × 4 minutes of HIIE on cycle ergometer with 3 minutes of active recovery between the bouts; control group relaxed for the time equivalent to intervention. fNIRS data was collected during the performance of the EF tests including Color Word Stroop Test (CWST) and Trail Making Test (TMT) in pre and post sessions in both the groups. Results indicated a significant change in the hemodynamic response in the form of increased oxygenated and decreased deoxygenated hemoglobin in the PFC areas specific to the EF tasks, with improved CWST and TMT scores in response to HIIE intervention. PFC activation was different in men and women in response to HIIE, however similar scores of task performance were observed in men and women during the performance of executive functions in response to HIIE. The study concludes that an acute HIIE session improves executive function which is associated with an increase activation of PFC. Sex differences exist in the activation of PFC in response to HIIE during EF processing. Our study adds to the current evidence regarding exercise and cognition.