This study aimed to examine the association of educational level with metabolic syndrome (MS) and its risk factors by gender in South Korea. A total of 6178 participants aged 20 years or older from The Fifth Korean National Health and Nutrition Examination Survey were included in this study. A generalized linear model and adjusted proportion were used to identify educational disparities in MS, its components, and its risk factors (smoking, high-risk alcohol consumption, obesity, and stress). In women, a clearly inverse association between education level and MS were observed with significant trend, and the decreasing trends of all risk factors across education quartiles were in line with the inverse association. However, the association between education level and MS was not observed with a significant trend among men. An opposite trend of risk factors across education levels was shown in men, with an increasing trend for obesity and decreasing trends for smoking and high-risk alcohol consumption. These findings demonstrate that obesity can explain gender differences in the association between education level and MS in South Korea.