The aim of this study was to examine the effects of repetitive transcranial magnetic stimulation (rTMS) on human brain activity. The effects of low-frequency magnetic stimulation were evaluated by analyzing the P300 component of event-related potentials (ERPs). A figure eight-shaped flat coil was used to stimulate the region over the left or the right supramarginal gyrus, which is considered to be the origin of the P300 component. We examined the effect of rTMS on the latency of the P300 component in 14 healthy individuals by applying 100 magnetic pulses for each stimulus point. Stimulus frequencies were 1.00, 0.75, 0.50, and 0.25 Hz rTMS. The auditory oddball task was used to elicit the P300s before and shortly after rTMS. We found that P300 latencies varied according to the stimulation frequency and the hemisphere of rTMS application. A 1.00 Hz rTMS pulse train over the left supramarginal gyrus shortened the P300 latencies by ∼15 ms at Fz. A 0.5 Hz rTMS pulse train over the left supramarginal gyrus lengthened the P300 latencies by ∼15 ms at Fz. In contrast, 0.75 and 0.25 Hz rTMS pulse trains over the left supramarginal gyrus and 1.00, 0.75, 0.50, and 0.25 Hz rTMS pulse trains over the right supramarginal gyrus did not alter P300 latencies. These results indicate that rTMS frequency affects cognitive processing. We suggest that the effects of rTMS vary according to the activity of excitatory and inhibitory synapses. In addition, the effects of rTMS over the left supramarginal gyrus are dependent on stimulus frequency.