Background: Allergic rhinitis is a symptomatic allergic disease of the nose that affects 10 to 20% of the global population. Chinese otolaryngologists use one acupuncture needle to stimulate the sphenopalatine ganglion because of its potential advantages for treating moderate-severe persistent allergic rhinitis compared with traditional Chinese acupuncture (verum acupuncture); however, little evidence is available to support the wide clinical use thus far. Therefore, we propose a protocol for a parallel, multicenter, assessor-blinded, randomized controlled trial to evaluate sphenopalatine ganglion stimulation with one acupuncture needle compared to verum acupuncture for treatment of moderate-severe persistent allergic rhinitis. Methods: In the trial, 96 patients previously diagnosed with moderate-severe persistent allergic rhinitis and meeting all inclusion criteria will be allocated to one of two equal therapeutic groups by using a computer-generated randomization list. The interventional group will receive sphenopalatine ganglion stimulation with one acupuncture needle for 4 weeks (once or twice weekly, total four to eight sessions); attending physicians will decide whether the second session is required in a week by examining signs and symptoms. The control group will receive individualized verum acupuncture for 4 weeks (twice weekly, total eight sessions). Follow-up evaluations will be performed 1 month later. The primary outcome measure is the change in the total nasal symptom score from the baseline to week 4. The secondary outcome measures include onset time and duration of effectiveness in every session, change in number of days with moderate-severe persistent allergic rhinitis from the baseline to week 8, change in total immunoglobulin E level and eosinophil count in venous blood from the baseline to week 4, change in Rhinoconjunctivitis Quality of Life Questionnaire score from the baseline to week 4, and clinical waiting time. Discussion: The trial should provide evidence for the benefits of sphenopalatine ganglion stimulation with one acupuncture needle for treating moderate-severe persistent allergic rhinitis, including better change in total nasal symptom score, faster onset time, longer duration of effectiveness, and shorter treatment time.