Seventeen refractory partial epilepsy patients were enrolled in an open-label study to evaluate the antiepileptic effect of low-frequency repetitive transcranial magnetic stimulation (rTMS). Seven of the patients had not obtained seizure-free status after epileptogenic focus resection surgery before they were enrolled in the study. All patients were treated with low-frequency rTMS which included 3 sessions per day (0.5 Hz, 90% RMT and 500 pulses each session) and lasted for 2 weeks. Seizure frequency, seizure days and epileptic discharges in the EEG obtained before, during and after stimulation were compared. The psychological conditions of all individual patients were evaluated with Symptom Checklist-90 (SCL-90) before and after rTMS treatment. Mean seizure frequencies per week significantly decreased in the following 4-week rTMS treatment period compared with the pretreatment period (14.09 vs. 5.63, p < 0.05, mean reduction of 60.02% in seizure frequency). Mean seizure days per week during the treatment period and the post-treatment period were lower than that of the pretreatment period (5.18 vs. 2.99 p < 0.05, mean reduction of 42.5% in seizure days). Mean epileptic discharges in the EEG decreased significantly during the treatment period compared to that of the pre-treatment period (78.60 vs. 66.09, p < 0.05, mean reduction of 15.9% in epileptic spikes discharges) in all 17 patients. Fourteen patients completed the test of Symptom Checklist-90 effectively. The scales of Global Severity Index, Depression, Anxiety, Phobic anxiety, Paranoid ideation, Psychoticism, Somatization, Obsession-compulsion, Interpersonal sensitivity, Hostility in patients decreased respectively at the post-treatment periods compared with those of the pre-treatment periods (P < 0.05). Low-frequency rTMS may have a significant antiepileptic effect in patients with refractory partial epilepsy. Additionally, our results indicate rTMS treatment can improve the psychological condition of these patients.