While many military positions are characterized by rigorous routines and long-hour shifts, some positions also require the practice of sensitivity and empathy alongside diligence and attention. Prolonged exposure to such conditions may promote emotional exhaustion, depersonalization and diminished self-accomplishment perception, all part of work-related burnout which may affect soldiers’ ability to practice their duty. The service in the Israel Defense Forces (IDF) checkpoint unit is an example of such conditions due to the soldiers’ constant interaction with civilian population. In this questionnaire-based cross-sectional study which included 404 responders from the IDF checkpoint battalions, we examined the effects of demographical, situational and personal variables on soldiers’ burnout. A hierarchical multivariate linear regression (R2 = 0.47) identified sense of coherence, the core concept in the salutogenic model of health, as the most prominent protective factor, followed by service motivation and perceived well-being (WB). Taken together, the results revealed several factors associated with military work-related burnout. These findings can serve as a base for burnout prevention programs, which may potentially improve not only the soldiers’ WB but also the interfaces between military and civilian populations.