The decline in healthy behavior in young people is a concern for public health in general and for country’s defense. The aim of this study is to identify and compare health behaviors and psychological distress between male conscripts enlisted and rejected for military service. This cross-sectional study included 1243 men aged 19–26 years (mean age 22.50 ± 2.43 years). We assessed health behaviors (physical activity, adherence to healthy eating patterns, cigarette smoking, and alcohol consumption) and psychological distress. Among all conscripts, 44.7% were physically inactive, 50.2% had low adherence to healthy nutrition, 9.6% were heavy drinkers, 62.3% were current smokers, and 9.1% had high psychological distress level. Compared with physically inactive conscripts, physically active conscripts were more likely to be enlisted (adjusted odds ratio (OR) = 1.42; 95% confidence interval (CI) 1.11–2.03). Compared with current nonsmokers, current smokers were less likely to be enlisted (OR = 0.58; CI 0.39–0.86). Compared with conscripts with a high distress level, those with a low distress level were almost four times more likely to be enlisted (OR = 0.26; 95% CI 0.12–0.55). Adherence to guidelines for healthy eating and alcohol consumption was not significantly related to enlistment. These findings suggest that health behaviors in male conscripts are unsatisfactory. That is, about half are physically inactive, have a poor diet, and smoke, and nearly one in 10 is a heavy drinker and has a high psychological distress level. The enlisted conscripts were more likely to be sufficiently physically active and less likely to be a current smoker or have a high distress level. Early intervention programs to provide a heathier population of young men for conscription should focus on mental well-being and target health-related behaviors such as physical activity and not smoking. Preferably, these should be implemented as health education programs in schools to help prevent the development of adverse health behaviors among young men. Governmental policies and strategies are required to enable intersectional collaboration and shared responsibility among the education, military and health sectors.