INTRODUCTION: Chronic pelvic pain syndrome (CPPS) is one of the most common concentrated pain conditions in urology and gynecology. Nearly one in seven women of worldwide suffer from CPPS each year. CPPS often requires a combination of treatments. An increasing number of studies have shown good therapeutic effects of rTMS on CPPS, however there is a lack of a reasonable treatment intensity reference.The main objective of this trial is to observe the effect of high-frequency rTMS at different intensities on CPPS.METHODS AND ANALYSIS: In this prospective, double-blinded randomized controlled trial of outcome assessment, a total of 63 female CPPS participants will be recruited and randomized (1:1:1) to high intensity rTMS, low intensity rTMS, and routinely treatment control group. The control group will be received a ten-day course of conventional pelvic floor rehabilitation, including pelvic floor muscle bioelectro-feedback therapy, pelvic floor magnetic therapy, Hydrosun light therapy. On the basis of conventional treatment, participants in the high intensity group will be received 10Hz with 110%RMT for a total of 15000 pulses; participants in the low intensity group will be received 10Hz with 80%RMT with 15000 pulses. Primary outcome includes visual analogue scale (VAS), The Female Urogenital Pain Index (GUPI), Zung self-rating anxiety scale (SAS) and Zung self-rating depression scale (SDS), and secondary indicators of pelvic floor muscle surface EMG will be measured at baseline and after completion of treatment.ETHICS AND DISSEMINATION: This study is approved by the Ethics Committee of Bao 'an People's Hospital, Shenzhen, Guangdong Province (approval number: BYL20211203). The results will be submitted for publication in peer-reviewed journals and disseminated at scientific conferences.TRIAL REGISTRATION: Chictr.org.cn, ID: ChiCTR2200055615. Registered on 14 January 2022, http://www.chictr.org.cn/showproj.aspx?proj=146720.