To evaluate the efficacy of Chinese medicine acupoint application (CMAA) combined with Western medicine for perennial allergic rhinitis (PAR) in children. In this prospective, parallel, randomized, placebo-controlled and single-blind trial from August to September, 2017, 180 children with PAR were randomly assigned to an integrative group (CMAA and Montelukast), CMAA group (CMAA and placebo tablet), or Montelukast group (placebo CMAA and Montelukast). Participants were applied with CMAA for 6 sessions over 2 weeks, and/or Montelukast Chewable Tablet orally once daily for 12 weeks. The changes in severity of symptoms were measured by Visual Analog Scale (VAS) and rhinitis control assessment test (RCAT) at 0, 2, 4 and 12 weeks of treatment. Blood samples were collected for serum interleukin-4, interferon gamma γ and T helper type 1 (Th1)/Th2 flow cytometric analysis at the time points of 0, 4 and 12 weeks. Eight cases dropped out from the trial, 3 in the integrative group, 2 in the CMAA group and 3 in the Montelukast group. The VAS scores decreased significantly while the RCAT scores increased significantly in all three groups at 4 and 12 weeks compared with baseline (P<0.01 or P<0.05). The VAS scores were significantly lower while the RCAT scores were significantly higher in the integrative and CMAA groups than the Montelukast group at 2 and 4 weeks (P<0.01 or P<0.05). At 2, 4 and 12 weeks, the scores of nasal congestion, sneezing, sleep problem, and rhinitis symptom control in the integrative and CMAA groups increased significantly compared with baseline (P<0.01 or P<0.05). The least percentages of Th2 and the most alleviated Th2 shift (highest Th1/Th2) were observed in the integrative group at 12 weeks compared with the other two groups (P<0.05). The combination of CMAA with Montelukast might be more effective and appropriate than either option alone for children with PAR. (Registered at Chinese Clinical Trial Register, registration No. ChiCTR-IOR-17012434).