The diagnostic process involves a series of stages in the patient pathway. Any errors or misleading information from any stage could lead to errors in the final decision-making. System dynamics modeling maps the diagnostic process as a whole and seeks to provide a quantitative way of analyzing different errors at each stage as well as relevant key factors. This paper provides a framework based on system dynamics for modeling the tracing of errors inside of the system from where errors initially occur, the routes of errors inside of the system, and how errors are delivered out of the system. Also, a detailed illustration of the phase history and physical examinations is provided as an example to explain how relevant factors can be interpreted and how this affects errors according to the framework.