The purpose of the present study was to use event-related potentials (ERP) to clarify the effect of magnetic stimulation on cognitive processing. A figure eight-shaped flat repetitive transcranial magnetic stimulation (rTMS) coil was used to stimulate either the region over the left or the right dorsolateral prefrontal cortex, which is considered to be the origin of the P300 component. Stimulus frequencies were 1.00, 0.75 and 0.50 Hz rTMS. The strength of the magnetic stimulation was set at 80% of the motor threshold for each participant. The auditory oddball task was used to elicit P300s before and shortly after rTMS, and comprised a sequence of sounds containing standard (1 kHz pure tone, 80% of trials) and deviant (2 kHz pure tone, 20% of trials) stimuli. We found that a 1.00 Hz rTMS pulse train over the left dorsolateral prefrontal cortex increased P300 latencies by 8.50 ms at Fz, 12.85 ms at Cz, and 11.25 ms at Pz. In contrast, neither 0.75 and 0.50 Hz rTMS pulse trains over the left dorsolateral prefrontal cortex nor 1.00, 0.75 and 0.50 Hz rTMS pulse trains over the right dorsolateral prefrontal cortex altered P300 latencies. These results indicate that rTMS frequency affects cognitive processing. Thus, we suggest that the effects of rTMS vary according to the activity of excitatory and inhibitory neurons in the cerebral cortex.