The aim of this study was to assess the age-standardized prevalence (prevalence) and age-standardized mortality (mortality) of congenital heart disease (CHD) by sex in Korean adults. Data were collected from the National Health Insurance Service in Korea from 2006 through 2016. The data consisted of main and secondary diagnoses related to CHD. We calculated the prevalence and mortality of CHD in adults with the direct method using the estimated Korean population in 2015 as the reference. The prevalence of CHD in Korean adults increased from 35.8 cases per 100,000 persons in 2006 to 65.6 cases in 2015. In 2015, the prevalence in the 20- to 44-year-old group, 45- to 64-year-old group, and the older than 65 years group was 54.6, 69.6, and 95.1 cases, respectively. Among women, the prevalence was 34.3 and 31.3 cases in men. The mortality of CHD in adults decreased from 3.061 persons per 100,000 persons in 2007 to 0.551 persons in 2015. The 5-year survival rate (SR) for people with CHD was 0.92 (95% confidence interval [CI] 0.91–0.93). The 5-year SR for the 20- to 44- and 45- to 64-year-old groups was more than 0.95; however, the 5-year SR of the older than 65 years group was only 0.73 (95% CI 0.72–0.74). The prevalence of CHD in Korean adults increased and the related mortality decreased during a decade. The 5-year SR of CHD for those over 65 years was lower than that for younger age groups.