Background: Primary dysmenorrhoea (PDM) is defined as a series of pain-dominated symptoms during and after menstruation without organic lesions. Non-steroidal anti-inflammatory drugs and oral contraceptives are usually recommended as first-line drugs for the clinical treatment of PDM, but their widespread long-term application is controversial. Radial extracorporeal shock wave therapy (rESWT) has been widely applied in musculoskeletal rehabilitation because of its secure and non-invasive characteristics and its confirmed effect in improving pain symptoms. This research seeks to explore the efficacy of rESWT for PDM and the changes in brain function of patients with PDM. Methods: This clinical research will be a randomised, evaluated blind and sham-controlled trial. Forty-six patients with PDM will be divided into the rESWT group (n = 23) and the sham rESWT group (n = 23) at random. In the rESWT group, treatment will be applied once within 48 hours of menstruation at six abdominal myofascial trigger points. The sham rESWT group will receive sham shockwave therapy on the same sites but without energy input. Other dysmenorrhoea-related treatments in both groups will be limited. The main indicators include the short-form McGill Pain Questionnaire and the Cox Menstrual Symptom Scale. The secondary indicators include the Zung Self-rating Anxiety Scale and Self-rating Depression Scale and functional magnetic resonance imaging (fMRI) changes in brain regions. Results will be evaluated at the screening, baseline and before and after treatment, and adverse treatments will be examined. Inter- and intra-group analyses will be performed in the statistics section. Discussion: This randomised controlled study is designed to explore the immediate efficacy of rESWT for PDM. After rESWT treatment, PDM symptom tests, pain tests as well as fMRI data will be investigated for the potential connections between immediate neuroanalgesic mechanisms, which are associated with pain and brain networks. The main results will be used to assess the efficacy of rESWT, and secondary results will focus on improving the neurobiological understanding of disease treatment.