Background: Well-being concerns among medical students are more prevalent than their age-matched peers in the United States. It remains unknown, however, if individual differences in well-being exist among U.S. medical students serving in the military. In this study, we sought to identify profiles (i.e., subgroups) of well-being in military medical students and examine the associations between these well-being profiles and burnout, depression, and intended retention in military and medical fields. Methods: Using a cross-sectional research design, we surveyed military medical students and then conducted latent class analysis to explore profiles of well-being, and applied the three-step latent class analysis method to assess predictors and outcomes of well-being profiles. Results: Heterogeneity in well-being was identified among the 336 military medical students surveyed, portraying medical students' falling into three distinct subgroups: High well-being (36%), low well-being (20%), and moderate well-being (44%). Different subgroups were associated with different risks of outcomes. Students in the subgroup of low well-being were at the highest risk of burnout, depression, and leaving medicine. In contrast, students in the moderate well-being group were at the highest risk of leaving military service. Conclusions: These subgroups may be clinically important as burnout, depression, and intention to leave medical field and/or military service occurred with varying likelihoods among medical students across the different well-being subgroups. Military medical institutions may consider improving recruitment tools to identify the best alignment between students' career goals and the military setting. Besides, it is crucial for the institution to address diversity, equity, and inclusion issues that may lead to alienation, anxiety, and a sense of wanting to leave the military community.