PURPOSE: This study investigated gender differences in the relationship between long working hours and metabolic syndrome. METHODS: Data based on the Sixth National Health and Nutrition Examination Survey (2014) pertaining to a total of 1,145 paid workers were analyzed. Working hours were divided into three groups (40–51 hours/week, 52–59 hours/week, ≥ 60 hours/week). The relationship between working hours and metabolic syndrome was then analyzed after adjusting for general and occupational characteristics, using a multiple logistic regression model. RESULTS: Working 40–51 hours per week was associated with the lowest metabolic syndrome among female workers (11.2%), whereas it was associated with the highest metabolic syndrome among male workers (28.0%). After adjusting for general and occupational characteristics, female workers working ≥ 60 hours per week showed odds ratios of 2.21 [95% confidence interval (1.07, 4.57)], compared to those who worked 40–51 hours per week. However, no clear association between long working hours and metabolic syndrome was found among male workers. CONCLUSIONS: The results suggest that working long hours, especially≥ 60 hours per week, is related to metabolic syndrome among female Korean workers.