We assessed the association between metabolic health and markers of inflammation and of endothelial dysfunction using data from the Ewha Birth and Growth Cohort Study. The data of 195 subjects aged 13–15 years were analyzed. To assess metabolic syndrome, continuous metabolic syndrome (cMets) scores were calculated. We measured the levels of high-sensitivity C-reactive protein (hs-CRP), intercellular adhesion molecule 1 (ICAM-1), and vascular cell adhesion molecule 1 (VCAM-1) as markers of inflammation and endothelial dysfunction. An increase of one SD in the cMets score resulted in a 1.25-fold (95% CI 1.10–1.42) increase in the risk of acute inflammatory status and a 1.26-fold (95% CI 1.11–1.43) increase in the risk of endothelial dysfunction as defined by ICAM-1, while VCAM-1 showed a meaningless trend. Of the metabolic components, body mass index (BMI) was positively associated with elevated hs-CRP levels and high-density lipoprotein cholesterol (HDL-c) levels were negatively associated with elevated ICAM-1 levels. Additionally, a mediation analysis showed that a high BMI was directly related to elevated hs-CRP levels and indirectly related to elevated ICAM-1 levels via HDL-c. Our findings show that poor metabolic health was related to an unfavorable inflammatory status and endothelial dysfunction in adolescents.