Information on sex differences in the association between chronotype and depression is scarce. We aimed to investigate these differences using data from the Korea National Health and Nutrition Examination Survey in 2016. Chronotypes were categorised based on mid-sleep time on free days corrected by sleep debt accumulated on workdays (MSFsc): early type, < mean MSFsc - 1 standard deviation (SD); intermediate type, between mean MSFsc - 1 SD and MSFsc + 1 SD; and late type, > mean MSFsc + 1 SD. A Patient Health Questionnaire-9 score of ≥ 10 indicated depression. Among 5550 non-shift working adults aged 19-80 years, the prevalence rates of depression in the early, intermediate, and late chronotype groups were 7.4%, 4.5%, and 9.3%, respectively. Women with late chronotype (odds ratio [OR] = 2.9, 95% confidence interval [CI] = 1.8-4.7) showed a higher risk of depression than women with intermediate chronotype after adjusting for covariates. Women with early chronotype did not show a significant difference in depression risk (OR = 1.3, 95% CI = 0.9-2.0). In conclusion, late chronotype is associated with an increased risk of depression in women but not in men. Early chronotype is not associated with depression in women or men.