Introduction: Military medical students enter residency through two main pathways: (1) The Uniformed Services University (USU) and (2) the Armed Services Health Professions Scholarship Program (HPSP). The purpose of this study was to compare how these two pathways prepare military medical students for residency. Methods: We conducted semi-structured interviews with 18 experienced military residency program directors (PDs) in order to explore their perceptions of the preparedness of USU and HPSP graduates. We used a transcendental phenomenological qualitative research design to bracket our biases and guide our data analysis. Our research team coded each of the interview transcripts. We then organized these codes into themes, which served as the results of our study. Results: Five themes emerged from our data regarding the residents' preparedness: (1) Ability to navigate the military culture, (2) understanding of the military's medical mission, (3) clinical preparation, (4) ability to navigate the Military Health System (MHS), and (5) teamwork. The PDs described how USU graduates better understand the military's medical mission and are more easily able to navigate the military culture and the MHS because of their lived experiences during military medical school. They also discussed the various levels of clinical preparation of HPSP graduates, in contrast to the USU graduates' more consistent skills and abilities. Finally, the PDs believed both groups to be strong team players. Conclusions: USU students were consistently prepared for a strong start to residency because of their military medical school training. HPSP students often experienced a steep learning curve because of the newness of the military culture and MHS.