To investigate the effects of low-frequency repetitive transcranial magnetic stimulation (rTMS) on patients with benign epilepsy with centrotemporal spikes (BECTS).In this open pilot study, we enrolled four BECTS patients who had frequent seizures (at least 3 seizures during the 3-month baseline). After localizing sources of interictal epileptiform discharges (IEDs) with magnetoencephalography, IEDs-source-rTMS (1 Hz) with 500 pulses at 90% of resting motor threshold was applied for 10 weekdays in each patient. The primary outcome measure was the seizure-reduction rate after rTMS. Other outcome measures were the spike-wave index (SWI), behavioral evaluation, and adverse effects.All four patients received at least 3 months seizure-free after rTMS. Compared with baseline, SWI decreased significantly after rTMS in three patients (patient 1, 3 and 4) (P = .002, P = .007, and P < .001, respectively). Attention deficit identified in two patients in baseline recovered to the normal range after rTMS. No adverse effect was observed.Our preliminary observation provides a promising approach to reducing clinical seizures for BECTS with frequent seizures. Of importance, our data may provide a potentially novel method for the high prevalence of behavioral problems in BECTS patients via decreasing cortical hyperexcitability.Copyright © 2022 The Authors. Published by Elsevier Inc. All rights reserved.