The combination of transcranial magnetic stimulation (TMS) and electroencephalogram (EEG) is an effective tool for investigating the functional connectivity in the brain. This paper investigated cortical reactivity and connectivity by the combination of TMS and EEG. Spontaneous activity of the brain was measured before and after magnetic stimulation. The effect of TMS on alpha activity was investigated. The alpha wave was suppressed for a few seconds after stimulation of the occipital area. No differences in the suppression of the alpha waves were found with and without auditory masking. Furthermore, the coil click of TMS had no effect on the alpha wave. The alpha wave was significantly suppressed by the occipital stimulation, whereas slight suppression was observed in other areas of stimulation. The alpha wave was increasingly suppressed as the stimulation magnitude became more intense. In order to investigate the evoked response by TMS, evoked potentials generated by TMS were measured. It was observed that more evoked responses spread to the center of the brain when the cerebellum was stimulated than at other areas of stimulation. These results indicated that TMS blocked the neural connections within alpha wave generation, and the electrical currents produced by TMS affected the neural activities.