The main purpose of this study is to examine the improvement and discourse of the medical education system in Korea since 1990. In particular, this study, focusing on the graduate medical education system initiated in 2002, has explored the discussions that led to the system’s establishment and what the context of those discussions. To meet this objective, this study analyzed research report related to the medical education system authored by members of the government and medical community, suggestions to the government, discussion materials, and data with regard to the Medical (Dental) Education Eligibility Test. The improvement of the medical education system in Korea has been an important issue in education reform by the expansion of the number of years of higher education, the requirements for increased levels of professional knowledge by improving public educational standards, and the basic formation policy of higher education consisting of graduate school, special graduate school, and professional graduate school. Nevertheless, the views of the government and the medical community on improving medical education system have made an obvious difference. This was due to different aims about how to improve the medical education system and different perception of the degree and medical education system. The medical community at least tended to prefer the status of academic positions over professional positions. The policy of medical education for people with a bachelor’s degree which was introduced in 2002 spread to many colleges of medicine based on the government’s administrative and financial support policy. Even so, the absence of accompanying policy by the relevant government agencies and department of education, which could have ensured the success of the system, has led to continued debate. In conclusion,without a consistent and persistent government policy, the graduate medical education system has led to confusion in many medical institutions. Above all, an evidence-based policy decision and policy approach based on a long-term perspective are necessary in order to improve the medical education system.