Background: In Korea, there have been no reports comparing the prevalence of major congenital anomalies with other countries and no reports on surgical treatment and long-term mortality. We investigated the prevalence of 67 major congenital anomalies in Korea and compared the prevalence with that of the European network of population-based registries for the epidemiological surveillance of congenital anomalies (EUROCAT). We also investigated the mortality and age at death, the proportion of preterm births, and the surgical rate for the 67 major congenital anomalies. Methods: Korean National Health Insurance claim data were obtained for neonates born in 2013–2014 and admitted within one-year-old. Sixty-seven major congenital anomalies were defined by medical diagnoses classified by International Classification of Diseases-10 codes according to the EUROCAT definition version 2014. Mortality and surgery were defined if any death or surgery claim code was confirmed until 2020. Poisson distribution was used to calculate the 95% confidence interval of the congenital anomaly prevalence. Results: The total prevalence of the 67 major anomalies was 433.5/10,000 livebirths. When compared with the prevalence of each major anomaly in EUROCAT, the prevalence of spina bifida, atrial septal defect (ASD), congenital megacolon, hip dislocation and/or dysplasia and skeletal dysplasia were more than five times higher in Korea. In contrast, the prevalence of aortic atresia/interrupted aortic arch and gastroschisis was less than one-fifth in Korea. The proportion of preterm births was 15.7%; however, more than 40% of infants with anencephaly, annular pancreas and gastroschisis were preterm infants. Additionally, 29.2% of the major anomalies were admitted to the neonatal intensive care units at birth, and 25.6% received surgical operation. The mortality rate was 1.7%, and 78.2% of the deaths occurred within the first year of life. However, in neonates with tricuspid valve atresia and stenosis, duodenal atresia or stenosis, and diaphragmatic hernia, more than half died within their first month of life. ASD and ventricular septal defect were the most common anomalies, and trisomy 18 and hypoplastic left heart syndrome were the most fatal anomalies. All infants with aortic atresia/interrupted aortic arch and conjoined twins received surgery. Conclusion: The proportion of surgeries, preterm births and mortality was high in infants with major congenital anomalies. The establishment of a national registry of congenital anomalies and systematic support by national medical policies are needed for infants with major congenital anomalies in Korea.