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North Korean Refugees (NKRs) undergo defection, and this has been shown to impact their current health status in South Korea. However, little is understood about how the defection process is related to metabolic syndrome (MetS). This study regarded the defection process to be a quasi-measurement of traumatic experience and investigated whether defection was a risk factor for MetS among NKRs living in South Korea. This cross-sectional study obtained data from the Korea University Anam Hospital in Seoul. NKRs (N = 847) voluntarily completed questionnaires and underwent at least one medical examination between October 2008 and July 2021. Multivariable logistic regression models were used to evaluate whether the number of countries transited by NKRs was associated with MetS by controlling for covariates. The prevalence of MetS among male and female NKRs in South Korea was 12.3% and 13.3%, respectively. The highest prevalence of MetS (33.4%) was among NKRs who had transited two countries. The number of months in transit countries (mean: 49.9 ± 51.7) and period of residence in South Korea (mean: 40.9 ± 40.9 months) were also considered. NKRs who transited three countries had a higher probability of MetS (odds ratio [OR] 2.660, 95% confidence interval [CI] 1.161–6.097) than those who travelled directly to South Korea. NKRs who transited three countries and had only resided in South Korea for a short period had a higher probability of MetS (OR 3.424, 95% CI 1.149–10.208) than those who have lived in South Korea for a longer period. Considering the social vulnerability of NKRs and consequential health problems, there is an urgent need for appropriate support from the government and society. [ABSTRACT FROM AUTHOR]