To investigate whether priming stimulation influences the responses of intracortical inhibitory and facilitatory motor circuits to a subsequent plasticity-inducing inhibitory theta burst TMS paradigm. Using standard transcranial magnetic stimulation (TMS) procedures, MEP amplitude, short-interval intracortical inhibition (SICI), and short-interval intracortical facilitation (SICF) were assessed at baseline and 5, 20 and 30 min following continuous theta burst stimulation (cTBS), intermittent TBS (iTBS), and iTBS-primed cTBS. SICI was assessed using paired-pulse TMS at inter-stimulus intervals (ISI) of 3 ms (SICI(3)) and the latency corresponding to the latency at which SICF was minimal in each individual. SICF was assessed at ISIs corresponding to Peak 1, Trough 1, Peak 2, and Peak 3 of each individual's SICF curve. When applied alone cTBS inhibited and iTBS facilitated MEP amplitudes. iTBS-primed cTBS resulted in greater MEP inhibition than cTBS alone. There were no changes in SICF and only marginal changes in SICI following any intervention. Synapses mediating MEP generation undergo modification following iTBS-primed cTBS, possibly through mechanisms related to metaplasticity or synaptic depotentiation. A lack of substantial changes in SICI and SICF under all experimental conditions suggests that the tested rTMS paradigms may be non-optimal for inducing robust modulation of the neural elements mediating SICI and SICF across subjects. Priming stimulation may provide an approach which facilitate neuroplastic change within the human motor cortex at least in circuits responsible for MEP generation.