Abstract Background Allergic rhinitis is one of the most common health complaints worldwide. Complementary and alternative medical approaches have been employed to relieve allergic rhinitis symptoms and to avoid the side effects of conventional medication. Acupuncture has been widely used to treat patients with allergic rhinitis, but the available evidence of its effectiveness is insufficient. Our objective is to evaluate the effectiveness of acupuncture in patients in Korea and China with persistent allergic rhinitis compared to sham acupuncture treatment or waitlist control. Methods This study consists of a multi-centre (two centres in Korea and two centres in China), randomised, controlled trial with three parallel arms (active acupuncture, sham acupuncture, and waitlist group). The active acupuncture and sham acupuncture groups will receive real or sham acupuncture treatment, respectively, three times per week for a total of 12 sessions over four weeks. Post-treatment follow-up will be performed a month later to complement these 12 acupuncture sessions. Participants in the waitlist group will not receive real or sham acupuncture treatments during this period but will only be required to keep recording their symptoms in a daily diary. After four weeks, the same treatment given to the active acupuncture group will be provided to the waitlist group. Discussion This trial will provide evidence for the effectiveness of acupuncture as a treatment for persistent allergic rhinitis. The primary outcome between groups is a change in the self-reported total nasal symptom score (i.e., nasal obstruction, rhinorrhea, sneezing, and itching) from baseline at the fourth week. Secondary outcome measures include the Rhinitis Quality of Life Questionnaire score and total non-nasal symptom score (i.e., headache, itching, pain, eye-dropping). The quantity of conventional relief medication used during the follow-up period is another secondary outcome measure. Trial registration Current Controlled Trials ISRCTN90807007