Background A single bout of high intensity cycling (~90% VO2peak) immediately after motor skill training enhances motor memory consolidation. It is unclear how different parameters of exercise may influence this process and the underlying mechanisms are poorly understood. We hypothesize that the effects of exercise on consolidation are time-dependent with a decreasing positive effect of exercise post acquisition and investigate the role of exercise intensity and timing on motor memory consolidation. Furthermore, we explore the potential role of transient changes in corticospinal excitability (CSE) accompanying skill learning and exercise. Methods Sixty able-bodied male subjects (20-35 years) were randomly assigned to one of five groups that practiced a visuomotor accuracy task. 20 min post motor skill learning (MSL), subjects in Experiment A performed either a single bout of aerobic exercise at 45% (EX45) or 90% (EX90) of peak oxygen consumption (VO2peak) or rested (CON). In Experiment B, two additional groups performed the same exercise protocol at 90% VO2peak at 1hour (EX90+1h) and 2 hours (EX90+2h) post MSL. Randomization was stratified to ensure that the groups were matched for VO2peak and baseline motor performance. Delayed retention tests of motor skill were tested 24 hours (R24) & 7 days (R7) post acquisition. Transcranial magnetic stimulation (TMS) was applied to the primary motor cortex to obtain measures of CSE, intracortical inhibition (SICI) and facilitation (SICF) before and after MSL, following exercise and in delayed retention tests. Motor-evoked potentials (MEPs) were recorded from the extensor carpi radialis muscle. Results Analysis of motor performance revealed no differences between groups during MSL, but differences in delayed retention tests. In Experiment A, EX90 showed a higher level of retention at R7 compared to CON. In Experiment B, EX90+2h demonstrated a level of retention at R24 and R7 equivalent to CON. Discussion In line with recent findings, the results show that exercise can promote motor memory consolidation. The results of Experiment A demonstrate that exercise intensity plays an important role for motor memory consolidation in favour of higher intensity aerobic exercise, while Experiment B indicates that timing of exercise is also important, with exercise immediately following motor skill learning being more efficient. Motor performance in retention tests were not related to measures of CSE at any time point indicating that further studies are necessary to understand the physiological mechanisms leading to improvements in motor memory relating to exercise.