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South Korea is one of the countries with the longest working hours in the OECD countries. Long working hours can be a risk factor of mental illness as well as cardiovascular disease. The aim of this study was to evaluate the effect of long working hours on depressive symptoms among employees in South Korea.This study used data from the Korea Working Conditions Survey in 2014. Study subjects included 22 910 employees aged 19 years or older who work more than 35 hours per week. Working hours were categorised into 35–40, 41–52, 53–68, and more than 68 hours per week. Depressive symptoms were assessed using the WHO’s Well-Being Index with cut-off score of 50. We calculated prevalence ratios of depressive symptoms according to working hours using log-binomial regression.Only 38.6% of Korean employees worked 35–40 hours per week. The proportion of employees who worked 41–52, 53–68, and more than 68 hours were 32.7, 15.4, and 4.7%, respectively. The rate of depressive symptoms was 42.8%, and the average of well-being index in Korea was 58.3. The longer the working hours were, the higher the risk of depressive symptoms was. Even after adjusting for sex, age, socioeconomic position, physical problems, job stress and exposure to violence, the risks of depressive symptoms were significantly higher in people who worked 53–68 hours/week (PR, 1.13 95% CI: 1.09 to 1.17), and more than 68 hours/week (PR, 1.07 95% CI: 1.02 to 1.13) than 35–40 hours/week.We showed the long working hours could be an independent risk factor for depressive symptoms in employees. Long working hours can lead to the lack of time to recover and sleep disturbances, which can be associated with depressive symptoms. It is necessary to adjust to the appropriate working hours for employees’ mental health.