BACKGROUND: Recently, the emergence of long working hours and the associated conditions such as coronary heart disease (CHD) and stroke have gained attention. The aim of this study was to investigate the association between long working hours and the 10-year-risk of CHD and stroke, estimated by Jee’s health risk-appraisal model for ischemic heart disease. METHODS: We analyzed data from Koreans who randomly enrolled in Korean National Health and Nutrition Examination Survey 2008–2012 and finally included 13,799 participants. The participants were classified as per their working hours: 0–30 h/week, 31–39 h/week, 40 h/week, 41–50 h/week, 51–60 h/week, 61–70 h/week, 71–80 h/week, and >80 h/week. The risks for CHD and stroke were determined using Jee’s health risk-appraisal model. Multiple logistic regression was used to analyze the association between working hours and 10-year risk for CHD. RESULTS: The 10-year risks for CHD and stroke were significantly and positively associated with working hours in both men and women. Furthermore, higher risks for CHD and stroke were associated with longer working hours in women. CONCLUSION: Long working hours are significantly associated with the risks of CHD and stroke, estimated by Jee’s health risk-appraisal model. This study suggests the need for proper management of working hours to reduce CHD risk and stroke risk in the Korean population. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s40557-016-0149-5) contains supplementary material, which is available to authorized users.