Acute aerobic exercise has been shown to improve fine motor skills and alter activation of the motor cortex (M1). The intensity of exercise may influence M1 activation, and further impact whole-body motor skill performance. The aims of the current study were to compare a whole-body motor skill via a piano task following moderate-intensity training (MIT) and high-intensity interval training (HIIT), and to determine if M1 activation is linked to any such changes in performance. Nine subjects (seven females and two males), aged 18 ± 1 years completed a control, MIT, and HIIT trial followed by administration of a piano performance task. M1 activation was evaluated by measuring oxyhemoglobin (O 2 Hb) and hemoglobin difference (Hbdiff) changes during post-exercise piano performance using functional near-infrared spectroscopy (fNIRS). The results indicate that piano performance scores were higher after the MIT trial, but not HIIT trial, compared to the control trial. A negative relationship was detected between heart rate during HIIT and post-HIIT piano scores. M1 activation (as measured by Hbdiff) was significantly increased after the HIIT trial. M1 activation was also positively associated with piano performance when exercise trials (HIIT + MIT) and all trials (HIIT + MIT + Control) were combined. We found that acute moderate-intensity exercise led to an improvement in complex motor skill performance while higher-intensity exercise increased M1 activation. These results demonstrate that moderate-intensity exercise can prime the nervous system for the acquisition of whole-body motor skills, suggesting that similar exercise protocols may be effective in improving the outcomes of other motor tasks performed during regular routines of daily life (e.g., sporting tasks, activities of daily living or rehabilitation). In addition, it appears that improvements in motor task performance may be driven by M1 activation. Our findings provide new mechanistic insight into the complex relationship between exercise intensity, M1 activation, and whole-body motor skill performance.