Background and Objectives Rural family physician is one of the strategic reforms in Iranian health system. It has been implemented since 2005 with the aim of improving people's access to health services. Despite its pivotal role in health system programs, the program has not progressed according to its original policies. Therefore, in this study, we aimed to identify the challenges of the rural family physician to provide solutions to these problems. Material and Methods The present study is in the field of qualitative studies. This was done by interviewing and reviewing the documentation. The sampling was purposive and the documents were systematically selected. In-depth semi-structured interviews were conducted with 26 key informants. Data were analyzed using MAXQDA software by content analysis method. Results After more than a decade of practicing family physician, the program still faces a number of key challenges in the areas of leadership and governance, financing, service providers, training and making culture, customer behavior, and monitoring and evaluation. Most of the program's challenges are related to leadership and governance, such as the negligible role of the private sector in service delivery, politicians are not justified about the program, and failure to anticipate the infrastructure required for the program. Conclusion Given the importance and key role of the family physician in the field of health and completing primary health care (PHC), especially the effective role in achieving UHC, with proper planning, appropriate and practical interventions should be designed and implemented to remove barriers and enhance the family physician program.