Abstract Background Allergic rhinitis is a common respiratory disease. Acupuncture is used to treat it in traditional Chinese medicine, and generally, the L120, ST2 and ST36 acupoints are selected in clinical practice. We report a new method of acupuncture at the sphenopalatine acupoint (SPA) for treatment of persistent allergic rhinitis (PAR). The effect of this treatment was investigated using two different needling depths. The efficacy of this treatment was associated with accurate stimulation of the sphenopalatine ganglion (SPG). Methods/Design A total of 61 patients diagnosed with PAR were randomly allocated to either the acupuncture or the sham acupuncture group. The difference between the groups was the needle depth when acupuncture was administered, which was 50 mm and 20 mm. Alteration in total nasal symptom score (TNSS) was the primary outcome. Quality of life, medication dosages and adverse events were secondary outcomes, measured using the Rhinoconjunctivitis Quality of Life Questionnaire (RQLQ). Confidence assessment was performed to evaluate data from the treatment and follow-up periods. Results Results were: (1) average TNSS in the treatment group was significantly lower than in the control group at week 4 (median and 25th and 75th percentiles were 5.00 (4.00, 7.00) and 8.00 (7.00, 10.00), respectively (P