Increasing evidence supports the use of physical activity for modifying brain activity and overall neurological health. Specifically, aerobic exercise appears to have a positive effect on cognitive function, which some have suggested to be a result of increasing levels of arousal. However, the role of aerobic exercise on movement‐related cortical activity is less clear. We tested the hypothesis that (1) an acute bout of exercise modulates excitability within motor areas and (2) transient effects would be sustained as long as sympathetic drive remained elevated (indicated by heart rate). In experiment 1, participants performed unimanual self‐paced wrist extension movements before and after a 20‐min, moderate intensity aerobic exercise intervention on a recumbent cycle ergometer. After the cessation of exercise, Bereitschaftspotentials (BP), representative cortical markers for motor preparation, were recorded immediately postexercise (Post) and following a return to baseline heart rate (Post[Rest]). Electroencephalography (EEG) was used to measure the BP time‐locked to onset of muscle activity and separated into three main components: early, late and reafferent potentials. In experiment 2, two additional time points postexercise were added to the original protocol following the Post[Rest] condition. Early BP but not late BP was influenced by aerobic exercise, evidenced by an earlier onset, indicative of a regionally selective effect across BP generators. Moreover, this effect was sustained for up to an hour following exercise cessation and this effect was following a return to baseline heart rate. These data demonstrate that acute aerobic exercise may alter and possibly enhance the cortical substrates required for the preparation of movement.