Background: As the number of people seeking to use traditional medicine to treat common diseases is increasing worldwide, the quantity of information that needs to be analyzed is also increasing. Traditional medicine is commonly used in South Korea and Taiwan for treating allergic rhinitis and is covered by the National Health Insurance in both countries. To date, there has been no nationwide comparison of traditional medicine used to treat patients with allergic rhinitis between these two countries. Methods: This study analyzed the National Health Insurance cohort database in 2011 from South Korea and Taiwan to compare the utilization pattern of traditional medicine in adult patients with allergic rhinitis. Results: During 2011, there were significantly more adult patients with allergic rhinitis using traditional medicine in Taiwan (9898/54,555, 18.1%) than in South Korea (533/11,761, 0.5%). Users of traditional medicine from both countries were more prevalent among women, the younger population aged 20–39 years, and among people who visited traditional medicine clinics more frequently than hospitals. The most common traditional medicine treatment modality for allergic rhinitis was acupuncture in South Korea, while powdered herbal preparations was most commonly used in Taiwan. Xiaoqinglong-tang (Socheongryongtong-tang) was the most commonly used herbal preparation in South Korea, while Xinyi-san (Sinyi-san) was the most commonly prescribed herbal preparation in Taiwan. Conclusion: An analysis of the National Health Insurance database of South Korea and Taiwan revealed different utilization patterns of traditional medicine in adult patients with allergic rhinitis between the two countries. We believe these phenomena are due to the difference in the national healthcare systems in both countries.