Since medical education programs in Korea and Japan seem to mutually influence each other, this review article provides a history of Japanese medical education, focusing on the way in which it influenced and was influenced by Korean medical education. In the late 19th century, the University of Tokyo established the core medical school, disseminating its scholarship and system to other medical schools. In the early 20th century, the balance between the quality and quantity of medical education became a new issue; in response, Japan developed different levels of medical school, ranging from imperial universities to medical colleges and medical vocational schools. After World War II, all of Japan’s medical schools became part of the university system, which was heavily regulated by the Ministry of Education (MOE) Standard for the Establishment of Universities. In 1991, MOE deregulated the Standard; since 2000, several new systems have been established to regulate medical schools. These new approaches have included the Model Core Curriculum, 2-year mandatory postgraduate training, and a medical education accreditation system. Currently, most medical schools are nervous, as a result of tighter regulatory systems that include an accreditation system for undergraduate education and a specialty training system for postgraduate education.