This study aimed to analyze the epidemiology of congenital upper limb anomalies (CULA) in Korea. We evaluated the incidence of each type of CULA, the presence of coexisting anomalies and the surgical treatment status in CULA patients. We conducted a retrospective cohort study of patients aged < 1 year between 2007 and 2016 who were registered with CULA in the Health Insurance Review and Assessment Service of Korea. In total, 10,704 patients had CULA, including 6,174 boys (57.7%) and 4,530 girls (42.3%). The mean annual incidence of CULA was 23.5 per 10,000 live births; it was significantly higher in boys than in girls (26.3 vs. 20.5, p < 0.001). Among the four categories of CULA-polydactyly, syndactyly, limb deficiency, and other anomalies-polydactyly was the most common. In total, 4,149 patients (38.8%) had other congenital anomalies and coexisting anomalies of the circulatory system (24.9%) were the most common. In total 4,776 patients (44.6%) underwent operative treatment for CULA within minimum three years of the diagnosis. The proportion of patients who underwent surgical treatment was significantly higher for polydactyly (73.4% vs. 16.8%, p < 0.001) and syndactyly (65.3% vs. 41.5%, p < 0.001), but it was significantly lower in limb deficiency (27.6% vs. 45.4%, p < 0.001) and other anomalies (10.0% vs. 69.8%, p < 0.001) than rest of CULA patients. Among the patients who had operations, 21.5% underwent multiple operations. The proportion of patients who underwent multiple operations was significantly higher in syndactyly (35.6% vs. 18.1%, p < 0.001), but it was significantly lower in polydactyly (4.0% vs. 95.5%, p < 0.001) and other anomalies (17.9% vs. 21.9%, p < 0.001) than rest of CULA patients. These results could provide a basis for estimating the national healthcare costs for CULA and the required number of CULA specialists.