Allergic rhinitis significantly impacts patients' quality of life, and allergen immunotherapy (AIT) offers an alternative to conventional treatments. This study compares the efficacy and safety of subcutaneous immunotherapy (SCIT) and sublingual immunotherapy (SLIT) for allergic rhinitis. A comprehensive search of PubMed, Embase, and ClinicalTrials.gov identified nine randomized controlled trials involving 780 patients (427 SCIT, 353 SLIT). The primary outcome was symptom score; secondary outcomes included medication score, symptom medication score, and local and systemic reactions. Results showed SCIT significantly reduced symptom scores compared to SLIT (Pooled SMD: -0.52, 95% CI: -0.60, -0.03, I2 =83%, P<0.05). However, SCIT patients experienced more severe systemic reactions (grade 3&4) than SLIT patients (Pooled SMD: 6.27, 95% CI: 1.47, 26.73, I2 =0%, P=0.01). Other outcomes were comparable between both groups. In conclusion, SCIT is slightly more effective than SLIT but is associated with a higher frequency of severe systemic reactions, guiding clinicians to tailor treatments to individual patient needs.