Provoked vestibulodynia (PVD) is a highly prevalent and debilitating condition yet its management relies mainly on non-empirically validated interventions. Among the many causes of PVD, there is growing evidence that pelvic floor muscle (PFM) dysfunctions play an important role in its pathophysiology. Multimodal physiotherapy, which addresses these dysfunctions, is judged by experts to be highly effective and is recommended as a first-line treatment. However, the effectiveness of this promising intervention has been evaluated through only two small uncontrolled trials. The proposed bi-center, single-blind, parallel group, randomized controlled trial (RCT) aims to evaluate the efficacy of multimodal physiotherapy and compare it to a frequently used first-line treatment, topical overnight application of lidocaine, in women with PVD. A total of 212 women diagnosed with PVD according to a standardized protocol were eligible for the study and were randomly assigned to either multimodal physiotherapy or lidocaine treatment for 10 weeks. The primary outcome measure is pain during intercourse (assessed with a numerical rating scale). Secondary measures include sexual function, pain quality, psychological factors (including pain catastrophizing, anxiety, depression and fear of pain), PFM morphology and function, and patients' global impression of change. Assessments are made at baseline, post-treatment and at the 6-month follow-up. This manuscript presents and discusses the rationale, design and methodology of the first RCT investigating physiotherapy in comparison to a commonly prescribed first-line treatment, overnight topical lidocaine, for women with PVD.