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This prospective longitudinal study assessed the effects of the course management system, EDU3, on the effectiveness of the dissemination of holistic health care and evidence-based medicine (EBM) courses. Between January 2014 and December 2021, delinked data (n = 354,229) from EDU3 were analyzed. In addition to analyzing the main educational team or seed teachers responsible for opening the courses, yearly changing trends in the number and teaching styles of courses, main participants, and the diversity of teaching activities were evaluated. EDU3 precisely announced the courses opened by non-doctor major departments, including departments of medical education, nursing, and medical research, for non-doctor medical personnel. Meanwhile, the system smoothly announced doctor major departments which opened courses for doctors. A 2 times/4.5 times parallel increase in holistic health care/EBM courses from institution to department and the yearly increasing trends in the number of these courses indicated the success of this system. This study revealed that centralized training of seed teachers motivated them to open diverse department-oriented teaching activities for holistic health care and EBM. The parallel increasing trends of the number of courses opened by the institution and departments indicated the effective dissemination of holistic health care and EBM from institution to department.