The history of NTU Hospital can be traced back to 1895, when Taiwan was ceded to Japan in the Treaty of Shimonoseki. The Japanese government then established the "Taiwan Hospital" in Dadaocheng, Taipei. In 1898, the hospital moved to Changde Street. Reconstruction began in 1912 and was completed in 1921, becoming the largest modern hospital in Southeast Asia at that time.

In 1897, the hospital established the "Native Physician Training Institute" and began to train local Taiwanese physicians, which later developed into National Taiwan University College of Medicine. In 1928, Taipei Imperial University was established, the medical education system was restructured in 1936, and in 1938, the Taipei Imperial University Hospital was officially established.

After World War II, Taipei Imperial University was renamed National Taiwan University, and the hospital was renamed "National Taiwan University Affiliated hospital". In 1949, President Fu Ssu-nien changed the name of the hospital to "National Taiwan University  Hospital."

Since 2004, NTU Hospital has taken over several hospitals and established five branches, including Yunlin, Beihu Hospital, Jinshan Hospital, Hsinchu Hospital, and Cancer Center, to expand medical services and continue to protect the health of Taiwanese people.