Background The appendix plays and important role to the human intestinal microbiota and immunity. Thus, appendectomy may alter immune function and intestinal biofilm. Allergic rhinitis is a common disease which is due to imbalance of TH2/TH1 cells and cytokine. The aim of this study was to evaluate the risk of allergic rhinitis after appendectomy in children. Methods The data source was the National Health Insurance Research Database (NHIRD), which is a large, population-based database in Taiwan. We collected 4013 patients who had undergone appendectomy (case group) between January 1,2000 and December 31st , 2018 and matched them with 16,052 patients who had not undergone appendectomy (control group) by sex and age using proportional propensity score (PSM) at a ratio of 1:4 after excluding patients with a diagnosis of allergic rhinitis in the year prior to appendectomy. In addition, Poisson regression and subgroup analyses were used to investigate the relative risk of development of allergic rhinitis after appendectomy in children. Results The relative risk of subsequent allergic rhinitis in patients who had undergone appendectomy was found to be higher (R.R= 1.24; 95% CI, 1.18-1.30; p< 0.001) than in patients who had never undergone appendectomy. Subgroup analysis showed the risk of allergic rhinitis after appendectomy were significantly higher in patients aged 6-11 years (HR=1.20; 95% CI,1.10-1.32, P<0.001) and 12-18 years (HR=1.25; 95% CI,1.17-1.33; P< 0.01), and for both genders (HR=1.24;95% CI,1.15-1.34;p< 0.001 for women; HR=1.23;95% CI,1.15-1.31;p< 0.001 for men), living place (Urban, HR=1.25; 95%CI,1.17-1.33; p<0.001) ( Suburban areas, HR=1.20; 95%CI,1.10-1.31; p< 0.001), and lower income groups (Conclusion Appendectomy was correlated with a 1.24-fold increased risk of developing allergic rhinitis in children, especially within 5-years of follow-up. Therefore, we suggest that the indication of appendectomy should be carefully evaluated to decide the best way to treat acute appendicitis.