Kinmen County Hospital was established on Mofang Street following the end of World War Two in 1945. The hospital was re-organized as a civilian clinic by a non-governmental charity group, then was once more incorporated into the government and renamed the Office of Health. In September 1950 it was renamed the Kinmen Public Medical Office, and in 1953 it was again re-organized as the Kinmen County Health Center, Fujian Province. In 1956 it was moved to its current site in Jinhu Town. In January 1976 it was reorganized once more by the Executive Yuan as Kinmen County Hospital and Affiliated Hospital.
When the government announced the lifting of martial law and the military administration ended battlefied experiments December 7, 1992, permission was received for the establishment of the Kinmen County Health Bureau and County Hospital of Fujian Province.
On Oct. 1, 2005, Kinmen County Hospital was restructured and merged in Taipei District Court with Huagangshi Department Hospital (the former Kinmen Military Hospital) to form Kinmen County Hospital under the Department of Health of the Executive Yuan.