Non-consciously perceived arrow stimuli can speed up responses to similar stimuli that are shortly presented after a masked prime. Yet response facilitation may turn into a delay at particular intervals between masked primes and targets. In this case, the lateralized readiness potential, as a measure of the time course of differential activation between the primed and the unprimed motor cortices, consistently yielded two consecutive maxima of opposite polarity, at 250 and at 350 ms after prime onset. To further explore the mechanisms underlying inverse priming, we used single-pulse transcranial magnetic stimulation (TMS) of the left or right primary motor hand area (M1). Lateralized changes in corticomotor excitability induced by the masked prime were probed by assessing the effect of priming on the amplitude of the TMS-induced motor-evoked potentials (MEPs). In two experiments, MEPs increased and decreased, respectively, in the hand primed by the masked arrows when TMS was given at 250 and at 350 ms after prime onset, confirming the expectation that MEP changes may indicate the response tendencies induced by the masked primes. Both effects were more distinct with TMS of the left M1. However, there were also some differences between the patterns of results in the two experiments. We propose that the left M1 is activated for preparation of both right- and left-hand movements, and we relate the present results to current hypotheses about the nature of inverse priming.