Integration of electroencephalographic (EEG) recordings and transcranial magnetic stimulation (TMS) provides a useful framework for quantifying stimulation-induced modulations of neural dynamics. Amplitude and frequency modulations by different TMS protocols have been previously investigated, but the study of stimulation-induced effects on EEG phase has been more limited. We examined changes in resting brain dynamics following single TMS pulses, focusing on measures in the phase domain, to assess their sensitivity to stimulation effects. We observed a significant, approximately global increase in EEG relative phase following prolonged (>20 min) single-pulse TMS. In addition, we estimated higher rates of phase fluctuation from the slope of estimated phase curves, and higher numbers of phase resetting intervals following TMS over motor cortex, particularly in frontal and centro-parietal/parietal channels. Phase changes were only significantly different from their pre-TMS values at the end of the stimulation session, which suggests that prolonged single-pulse TMS may result in cumulative changes in neural activity reflected in the phase of the EEG. This is a novel result, as prior studies have reported only transient stimulation-related effects in the amplitude and frequency domains following single-pulse TMS.