Abstract The occurrence of dynamic changes in spontaneous electroencephalogram (EEG) rhythms in the awake state or sleep is highly variable. These rhythms can be externally modulated during transcranial magnetic stimulation (TMS) with a perturbation method to trigger oscillatory brain activity. EEG-TMS co-registration was performed during standard wake, during wake after sleep deprivation and in sleep in six healthy subjects. Dynamic changes in the regional neural oscillatory activity of the cortical areas were characterized using time-frequency analysis based on the wavelet method, and the modulation of induced oscillations were related to different vigilance states. A reciprocal synchronizing/desynchronizing effect on slow and fast oscillatory activity was observed in response to focal TMS after sleep deprivation and sleep. We observed a sleep-related slight desynchronization of alpha mainly over the frontal areas, and a widespread increase in theta synchronization. These findings could be interpreted as proof of the interference external brain stimulation can exert on the cortex, and how this could be modulated by the vigilance state. Potential clinical applications may include evaluation of hyperexcitable states such as epilepsy or disturbed states of consciousness such as minimal consciousness.