Introduction: Epilepsy has been known as a chronic brain disorder, influences large number of population around the world. Seizures should be treated as soon as possible to avoid the development of chronic epilepsy. Furthermore, there are some complications following surgical resection of epileptic focus and drug treatment. Transcranial magnetic stimulation has been suggested to generate current flow in the brain and could be an alternative to drug treatment or surgery. We study the protective effects of repetitive transcranial magnetic stimulation (rTMS) on seizure attacks and cellular damage in the amygdala in rats. Materials and Methods: In the present study four groups of rats including intact, pentylenetetrazole, rTMS+pentylenetetrazole and rTMS were used to investigate rTMS effects on cellular activity and seizure attacks in a model of epilepsy. The rTMS was applied for a month and then seizures was induced by intraperitoneally injection of pentylenetetrazole and seizure scores were determined. Finally, rats were killed and neuronal injury was evaluated in the amygdala. Results: Seizure scores as well as histological assessment revealed a significant reduction on seizure attacks and the mean number of necrotic cells in the amygdala following rTMS application. Conclusion: This study advocated a protective effect of rTMS on cellular structure in epilepsy. However, safety of rTMS in clinical practice need further investigations.