When the GHQ was established in the winter of 1944, at the height of the War of Resistance against Japan, it was called the Military Affairs Committee. It was founded to meet the needs of the resistance coalition and to restrain the spread of Japanese influence on the Mainland and in eastern and southern Asia. Its main branch, located in Kunming, assumed responsibility for coordinating directives and training for the western and southern battle districts. After the defeat of the Japanese, the Military of Defense assumed responsibility for running the army, navy, air force and logistics headquarters. The army HQ was recomposed of the Military Affairs Committee’s training division.

In October of 1949, as the situation on the Mainland fell into chaos, the GHQ was attacked by the communist forces. A small number of personnel were able to board planes and head for Taiwan. A second group of personnel traveled to Taiwan via Vietnam, while those remaining dispersed. At this point, the GHQ ceased to exist.

On March 1,1950, Chiang Kai-sheik, reacting quickly to popular opinion, resumed the Presidency. He was determined to reconsolidate the military and implement counter-attack preparations. That same month, the Ministry of Defense was reorganized, and it was decided to reinstate the army GHQ. On April 16, the GHQ, a reconfiguration of the Taiwan Defense Headquarters, was instilled at Fen Shan. In September of 1950, the GHQ was relocated to Taipei, where it remained until the Northern Anchor exercises of 1976 .Presently, the GHQ is in Tao Yuan.