Combined transcranial magnetic stimulation/electroencephalography (TMS/EEG) was used to study the activation and interaction of cortical regions to a variety of focused sub- and suprathreshold magnetic pulses over the left primary motor cortex (M1) in ten healthy subjects. Five single-pulse TMS conditions were performed based on the individual resting motor threshold (RMT): (1) 80%; (2) 100%; (3) 120%; (4) 130%; and (5) sham. Simple self-paced movements of the right first finger were also executed. We evaluated the reactions to magnetic stimulation and movement conditions using event-related power and event-related coherence transformations of alpha and beta rhythms. Event-related power reflected regional oscillatory activity of neural assemblies, while event-related coherence reflected the inter-regional functional coupling of oscillatory neural activity. The event-related power transformation revealed that the magnetic pulse modulated cortical oscillations within the first half second for both frequency ranges. For the alpha rhythm, threshold TMS induced a small decrease in the amplitude of EEG oscillations over the stimulation site, while for both rhythms, a progressive synchronization was observed as the intensity of TMS was increased in both hemispheres. Movement onset produced a greater bilateral decrease of power compared with the effects of a magnetic pulse. The event-related coherence revealed that TMS enhanced the electrode connectivity of both hemispheres. Additionally, it was more enhanced within the first 500 ms following stimulation and was seen only for the alpha frequency rhythm. The increase of functional connectivity between cortical areas was minor for magnetic stimulation conditions compared with that for finger movements. The single-pulse TMS over M1 partially modulated the motor cortex generators of oscillatory activity, while a simple active self-paced movement of the right first finger induced greater cortex activation and coupling between cortical regions. We propose that finger movements impose higher functional demands on the motor system compared to artificial magnetic stimulation. These findings are consistent with the possibility that the human motor system may be based on network-like oscillatory cortical activity and might be modulated by brief electromagnetic sub- and suprathreshold pulses applied to M1, suggesting a phenomenon of resetting.