Screening for secondary hypertension (HTN) is recommended for early-onset HTN. However, there have been few studies on secondary HTN in young adults. We aimed to investigate the prevalence and risk factors for secondary HTN in young male military personnel. In this retrospective cross-sectional study, hypertensive men (age, 19-29 years) were identified using the electronic medical records (EMR) database between 2011 and 2017. Among them, patients with secondary HTN were confirmed through a review of the EMR. Using clinical characteristics and laboratory findings, independent predictors associated with secondary HTN were identified by binary logistic regression analysis. Secondary HTN was confirmed in 140 of 6373 participants (2.2%). Overall, the most common causes were polycystic kidney disease (n = 47, 0.74%) and renal parenchymal diseases (n = 24, 0.38%). The independent predictors of secondary HTN were abnormal thyroid function test (TFT) (odds ratio [OR]: 9.50, 95% confidence interval [CI]: 4.84-19.45, P 0.001), proteinuria (\ge trace) (OR: 6.13, 95% CI: 2.97-12.99, P 0.001), hematuria (\ge trace) (OR: 4.37, 95% CI: 2.15-9.01, P 0.001), severe HTN (\ge 180/110 mmHg) (OR: 3.07, 95% CI: 1.42-6.65, P = 0.004), and non-overweight (OR: 3.03, 95% CI: 1.69-5.26, P 0.001). However, there were no significant differences in the family history of HTN, headache, total cholesterol, and diabetes between patients with primary and secondary HTN. Therefore, to ensure cost-effectiveness, screening for secondary HTN in young hypertensive men should be performed selectively considering abnormal TFT, proteinuria, hematuria, severe HTN, and non-overweight.