Reducing socioeconomic inequalities in health has become an important health policy agenda. This study aimed to measure socioeconomic inequalities in health in Korea over the past two decades and identify the contributing factors to the observed inequalities. Data from the Korea National Health and Nutrition Examination Survey (KNHANES) from 1998 to 2016/2018 were utilized. The concentration index (CI) was calculated to measure health inequalities, and decomposition analysis was applied to identify and quantify the contributing factors to the observed inequalities in health. The results indicated that health inequalities exist, suggesting that poor health was consistently more concentrated among Korean adults with lower income (1998: −0.154; 2016/2018: −0.152). Gender-stratified analyses also showed that poor health was more concentrated in lower income women and men, with the degree of inequalities slightly more pronounced among women. The decomposition approach revealed that income and educational attainment were the largest contributors to the observed health inequalities as higher income and education associated with better self-rated health. These findings suggest the importance of considering socioeconomic determinants, such as income and education, in efforts to tackling health inequalities, particularly considering that self-rated health is a predictor of future mortality and morbidity. Furthermore, it is essential to implement more egalitarian social, labour market, and health policies in order to eliminate the existing socioeconomic inequalities in health in Korea.