A medical student's career choice directly influences the physician workforce shortage and the misdistribution of resources. First, individual and contextual factors related to career choice have been evaluated separately, but their interaction over time is unclear. Second, actual career choice, reasons for this choice, and the influence of national political strategies are currently unknown in Switzerland. The overall objective of this study is to better understand the process of Swiss medical students' career choice and to predict this choice. Our specific aims will be to examine the predominately static (ie, sociodemographic and personality traits) and predominately dynamic (ie, learning context perceptions, anxiety state, motivation, and motives for career choice) variables that predict the career choice of Swiss medical school students, as well as their interaction, and to examine the evolution of Swiss medical students' career choice and their ultimate career path, including an international comparison with French medical students. The Swiss Medical Career Choice study is a national, multi-institution, and longitudinal study in which all medical students at all medical schools in Switzerland are eligible to participate. Data will be collected over 4 years for 4 cohorts of medical students using questionnaires in years 4 and 6. We will perform a follow-up during postgraduate training year 2 for medical graduates between 2018 and 2022. We will compare the different Swiss medical schools and a French medical school (the University of Strasbourg Faculty of Medicine). We will also examine the effect of new medical master's programs in terms of career choice and location of practice. For aim 2, in collaboration with the Swiss Institute for Medical Education, we will implement a national career choice tracking system and identify the final career choice of 2 cohorts of medical students who graduated from 4 Swiss medical schools from 2010 to 2012. We will also develop a model to predict their final career choice. Data analysis will be conducted using inferential statistics, and machine learning approaches will be used to refine the predictive model. This study was funded by the Swiss National Science Foundation in January 2023. Recruitment began in May 2023. Data analysis will begin after the completion of the first cohort data collection. Our research will inform national stakeholders and medical schools on the prediction of students' future career choice and on key aspects of physician workforce planning. We will identify targeted actions that may be implemented during medical school and may ultimately influence career choice and encourage the correct number of physicians in the right specialties to fulfill the needs of currently underserved regions. DERR1-10.2196/53138.