Aims: Converging evidence indicates beneficial effects of aerobic exercise on motor learning performance. Underlying mechanisms might be an impact of aerobic exercise on neuroplasticity and cortical excitability. Evidence suggests that motor learning and cortical excitability alterations correlate with the intensity of aerobic exercise and the activity level of participants. Thus, this study aims to investigate the effects of different aerobic exercise intensities on motor learning and cortical excitability in healthy individuals. Methods: The study was conducted in a cross-over and double-blind design. 26 healthy individuals (13 women and 13 men) performed a motor learning task and received cortical excitability assessment before and after a single session of low-, moderate-, high-intensity aerobic exercise or a control intervention. Results: The study revealed that motor learning performance and cortical excitability were significantly enhanced in the moderate-intensity aerobic exercise, compared with the other conditions. Conclusions: These findings suggest aerobic exercise intensity–dependent effects on motor learning in healthy adults. Underlying mechanism might be an exercised-induced alteration of cortical excitability, specifically a reduction of GABA activity.