Purpose: To evaluate the feasibility, efficacy, and safety of repetitive transcranial magnetic stimulation (rTMS) in patients with treatment-resistant chronic prostatitis/chronic pelvic pain syndrome (CP/CPPS). Methods: Eleven patients with CP/CPPS were enrolled in this prospective clinical study. rTMS was performed for 5 consecutive days in 20-minute sessions. Patients were evaluated at baseline, after treatment, and at 1, 4, 8, and 12 weeks after the last session with questionnaires concerning pain (numerical rating scale [NRS], the National Institutes of Health Chronic Prostatitis Symptom Index [NIH-CPSI], and the Short Form-36 [SF-36]), urinary symptoms (NIH-CPSI, Danish Prostatic Symptom Score [DAN-PSS-1]), quality of life (NIH-CPSI, SF-36), and psychometrics (Beck Depression Index [BDI]). Telephone-based interviews were used to evaluate side effects, subjective response, and changes in drug consumption. Results: All patients completed the planned treatment and follow-up according to protocol. No patients experienced serious side effects or significant pain increase during or after treatment. Mild transient tension headache responsive to oral pain medication was reported by 2 patients. Decreased pain was observed on the NRS after treatment and at 1 and 8 weeks (P=0.019, P=0.006, P=0.042, respectively) and on the NIH-CPSI pain domain at 1 week (P=0.04). Improvement in lower urinary tract symptoms was observed after treatment in the NIH-CPSI urinary domain (P=0.02) but not with the DANPSS-1. No significant changes in the BDI were observed. Nine patients reported a positive overall subjective response (82%) and 6 patients (55%) were able to reduce pain medication. Higher age was associated with lower NRS scores after treatment (R=0.605, P=0.048) and at 8 weeks (R=0.659, P=0.028). Conclusions rTMS for patients with CP/CPPS seemed to be well tolerated, at least moderately effective in pain reduction, and might be of interest in patients with chronic pelvic pain resistant to conventional treatment. These findings remain to be confirmed by a randomized trial.