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Background Vulvodynia, or vulvar pain, is a common condition in women; however, there are few evidence-based clinical trials evaluating nonpharmacological therapies for this condition. Acupuncture is one complementary and integrative medicine therapy used by some patients with vulvodynia. This study evaluates two different acupuncture strategies for the treatment of vulvodynia and aims to evaluate whether either of the acupuncture protocols reduces vulvar pain, pain duration or pain with intercourse. The study also examines how long the effect of acupuncture lasts in women with vulvodynia. Methods/design The study is designed as a randomized controlled trial, focused on two acupuncture protocols. Fifty-one patients who have had vulvodynia for more than 3 months will be recruited. Among them, 34 patients will be randomized into Groups 1a and 1b; those who are unwilling to receive acupuncture will be recruited into the standard care group (Group 2). Patients in Group 1a will have acupuncture focused on the points in the pudendal nerve distribution area, while patients in Group 1b will receive acupuncture focused on traditional (distal) meridian points. Patients in Group 2 will receive routine conventional treatments, such as using pain medications, local injections and physical therapies or other nonsurgical procedures. Acupuncture will last 45 min per session, once or twice a week for 6 weeks. The primary outcome measurement will be objective pain intensity, using the cotton swab test. The secondary outcome measurement will be subjective patient self-reported pain intensity, which will be conducted before cotton swab test. Pain intensities will be measured by an 11-point Numeric Pain Rating Scale. Pain duration and pain score during intercourse are recorded. Local muscle tension, tenderness and trigger points (Ashi points) are also recorded. All measurements will be recorded at baseline (before the treatment), at the end of each week during treatment and at the end of the 6 weeks. Follow-up will be done 6 weeks following the last treatment. Discussion Results of this trial will provide preliminary data on whether acupuncture provides better outcomes than nonacupuncture treatments, i.e., standard care, and whether acupuncture focused on the points in pudendal nerve distribution, near the pain area, has better results than traditional acupuncture focused on distal meridian points for vulvodynia. Trial Registration: Clinicaltrials.gov: NCT03481621. Register: March 29, 2018.