Although allergic rhinitis is not life threatening, it significantly influences the quality of a patient's life. This study is intended to evaluate the safety and efficacy of phototherapy with low-level energy of a 650 nm laser irradiation system in perennial allergic rhinitis patients. This clinical trial was an open-label, single-center study with 42 perennial allergic rhinitis subjects. Following laser irradiation in the nasal cavity with a laser irradiation system, the efficacy at weeks 1 through 4 was determined. The symptoms were scored with four parameters (nasal obstruction, rhinorrhea, sneezing and itching) before and after illumination of the laser, and the total score was recorded. A survey of Rhinoconjunctivitis Quality of Life Questionnaire (RQLQ) was conducted by patients before and after treatment. Following treatment, significant improvement in the clinical symptoms of nasal obstruction (P < 0.001), rhinorrhea (P = 0.005), sneezing (P = 0.001) and itching (P = 0.003) was reported by 68% of perennial allergic rhinitis patients. The overall RQLQ scores significantly improved by 45% from the baseline with the treatment after 4 weeks. These results indicate that phototherapy is an effective modality for treating perennial allergic rhinitis and is another option in the steroid-free management of immune-mediated mucosal diseases.