Physician shortages are more pronounced in rural than in urban areas. The geography of medical school application and matriculation could provide insights into geographic differences in physician availability. Using data from the Association of American Medical Colleges (AAMC), we conducted geospatial analyses, and developed origin-destination (O-D) trajectories and conceptual graphs to understand the root cause of rural physician shortages. Geographic disparities exist at a significant level in medical school applications in the US. The total number of medical school applications increased by 38% from 2001 to 2015, but the number had decreased by 2% in completely rural counties. Most counties with no medical school applicants were in rural areas (88%). Rurality had a significant negative association with the application rate and explained 15.3% of the variation at the county level. The number of medical school applications in a county was disproportional to the population by rurality. Applicants from completely rural counties (2% of the US population) represented less than 1% of the total medical school applications. Our results can inform recruitment strategies for new medical school students, elucidate location decisions of new medical schools, provide recommendations to close the rural-urban gap in medical school applications, and reduce physician shortages in rural areas.