The establishment of National Yang-Ming Medical College was approved by the Executive Yuan in January 1971. Yang-Ming was selected by the late President Chiang Kai-Shek in memory of the venerable Chinese scholar Wang Yang-Ming of the Ming Dynasty. In January 1974, Laboratory Building–the universitys first buildingwas completed, hence commenced the history of a glorious line of education with the first class of medical students to enroll in 1975. In compliance with the governments policy to solve medical shortage in Taiwans rural and mountainous regions, the Faculty of Medicine dedicated in the early years its education solely to training public doctors to serve the countrys need.

In May 15, 1975, Dr. Paul Han was appointed the first Provost of the College, therefore set the University Day. The first 120 students enrolled to the campus in July of the same year. Lacking its own hospital, the Veterans General Hospital in Taipei (VGHTPE) was later approved by the Executive Yuan to serve as Yang-Mings teaching hospital in order to provide both basic and clinical training.

In 1983 the Faculty of Medicine for post-Baccalaureate was established. This program aimed to improve medical research and service by attracting students with a bachelors degree from diverse backgrounds. As an encouragement, students in this program were initially subsidized 100% by the government until 1985. In 1987 this program was discontinued because the original goals were seemingly not satisfied.

Dynamic changes in the demand for physicians in Taiwans rural regions prompted the university to enlist self-funded students since 1988. Furthermore, financial subsidy to government-sponsored students that had been provided by the Ministry of Education was continued by the Department of Health since August 1992.

In July 1994, National Yang-Ming Medical College was renamed National Yang-Ming University (NYMU), granted by the Ministry of Education. This was the first university in Taiwan that focused mainly on the development of biomedical sciences. The original Faculty of Medicine became one of the subordinate organizations of the School of Medicine, and the college provost, Dr. Shao-Hua Han became the first President of NYMU. At the creation of the university, Yang-Ming only had three schools, six faculties, and nineteen post-graduate institutes. Today NYMU has five schools, seven faculties, and twenty-six post-graduate institutes, covering a broad scope of modern biomedical sciences and providing every student with the most ideal environment for learning.

In 1997 the two-year internship requirement for the 6th and 7th year students was replaced with four-month apprenticeship and 19-month internship. During the internship period students may opt to be trained in teaching hospitals other than VGH for four months. In 2002 the apprenticeship requirement was extended to six months, the internship reduced to 17 months, while the option for students to attempt at another hospital remained unchanged.

In 1999, the Faculty of Medicine for the first time launched the problem-based learning (PBL) to clinical and experimental diagnostic courses, and later extended to pathological curriculum. In 2001 the integrated clinical studies became available for the 4th year medical students. An innovated academic program involving seven years of medical learning/training was initiated in 2002. The first two years are general education, mainly concerning the humanities and physician-patient relationship. The basic medical training, integrated with PBL, begins in the third year and intensifies in the fourth. Students in the 5th and 6th year are required to go through the advanced medical lectures and apprentice in VGHTPE. The final year is a one-year internship in which students will receive practical training either in VGHTPE or other qualified teaching hospital in Taiwan.

National Yang Ming Chiao Tung University was created in 2021 through the merger of two universities: National Yang-Ming University and National Chiao Tung University.