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Transcranial magnetic stimulation (TMS) is a noninvasive brain stimulation method that modulates brain activity by inducing electric fields in the brain. Real-time, state-dependent stimulation with TMS has shown that neural oscillation phase modulates corticospinal excitability. However, such motor evoked potentials (MEPs) only indirectly reflect motor cortex activation and are unavailable at other brain regions of interest. The direct and secondary cortical effects of phase-dependent brain stimulation remain an open question. In this study, we recorded the cortical responses during single-pulse TMS using electroencephalography (EEG) concurrently with the MEP measurements in 20 healthy human volunteers (11 female). TMS was delivered at peak, rising, trough, and falling phases of mu (8–13 Hz) and beta (14–30 Hz) oscillations in the motor cortex. The cortical responses were quantified through TMS evoked potential components N15, P50, and N100 as peak-to-peak amplitudes (P50-N15 and P50-N100). We further analyzed whether the prestimulus frequency band power was predictive of the cortical responses. We demonstrated that phase-specific targeting modulates cortical responses. The phase relationship between cortical responses was different for early and late responses. In addition, pre-TMS mu oscillatory power and phase significantly predicted both early and late cortical EEG responses in mu-specific targeting, indicating the independent causal effects of phase and power. However, only pre-TMS beta power significantly predicted the early and late TEP components during beta-specific targeting. Further analyses indicated distinct roles of mu and beta power on cortical responses. These findings provide insight to mechanistic understanding of neural oscillation states in cortical and corticospinal activation in humans.