U.S. military Service members have consistently smoked more than the general population and the prevalence of smoking is even higher among U.S. veterans. Our study examined cigarette smoking patterns among Service members before and after military separation to better understand the disproportionate rate of smoking among veterans. Data from the Millennium Cohort Study were used. All study participants were in the military at baseline and some transitioned from the military to civilian life during the observation period. We investigated any impact of military separation on smoking, as well as other potential risk factors for smoking. Overall, we observed higher smoking prevalence among veterans than Service members. Additionally, we found that Service members smoked more while approaching their separation from the military. Longitudinal analysis revealed military separation was not a risk factor for smoking, as we had hypothesized. Baseline smoking was the most influential predictor of current smoking status. Other significant factors included alcohol consumption, life stressors, and mental health conditions, among others. Military separation was not a risk factor for smoking. However, Service members in the process of transitioning out of the military, as well as high alcohol consumers and Service members with mental health conditions, may be at higher risk of smoking. Including smoking prevention/cessation programs in pre-separation counseling sessions and developing smoking screening and cessation programs targeting specific high-risk subgroups may reduce smoking among Service members and veterans.