The benefits of physical exercise on brain function and its metabolism are well documented, and it is established that acute aerobic exercise could enhance executive function. The aim of this study was to report the effect of exercise intensity during acute intermittent exercise (IE) on executive function and heart rate outcomes. Twenty male subjects performed a series of six consecutive 3-min bouts of exercise at either 60 or 95% of peak power output (PPO), interspersed by 3 min of passive recovery on a bicycle ergometer. Reaction time (ms) and accuracy (%) of switching task using a computerized Stroop task were recorded before and after warm-up, after each bout of exercise and every 15 min during a 1-h passive recovery following exercise. A two-way repeated measures ANOVA was performed to quantify the effects of exercise time (bouts) and condition (exercise intensity). The ANOVA revealed a main effect of time and an interaction between intensity and time for the heart rate and heart rate variability, RPE, and perceived difficulty of cognitive tasks (p < 0.05). The session at 95% PPO induced a more important subjective and objective fatigue than at 60%. Also, participants found the switching task more difficult after the third repetition at 95% and throughout the repetition of the task during IE. Compared to baseline, cognitive performance was improved at both intensities (main effect of time; p < 0.05). However, IE at 60% induced lower reaction time (ES = − 1.1) than at 95% (ES = − 0.7). The decrease in reaction time persisted during the recovery period, following IE at 60% but returned to baseline 30 min after the IE at 95%. Our results demonstrate that both moderate and high exercise intensity enhance cognitive performance during and following IE. The greater perceived exertion and lower parasympathetic activity during exercise at 95% PPO could be responsible for the smaller improvement on reaction time, when compared to exercise at 60% PPO.