The unit was originally established in 1906 as the Kwantung Garrison to defend the Kwantung Leased Territory and the areas adjacent to the South Manchurian Railway. Composed of an infantry division and a heavy siege artillery batallion, it was stationed within the Kwantung Leased Territory. Supplementing this force were six independent garrison battalions as railway guards deployed along the railway zone, making a total troop strength of 10,000 men. Since the reorganization of 1919, this military unit was called the Kwantung Army.
Although the Kantogun was nominally subordinate to the Japanese High Command, its leadership demonstrated significant self-determination, as conspirators in the Army plotted the assassination of Zhang Zuolin in 1928 and the Manchurian Incident (1931) leading to the foundation of Manchuguo in 1932. The Army was heavily augmented, by up to 700,000 troops in 1941, to defend the whole territory of Manchuria and Inner Mongolia. Generals and young officers virtually controlled the puppet government of Emperor Pu Yi.
The Army fought against the Soviet Union's Red Army at Zhanggufeng in 1938 and Nomonhan in 1939, sustaining heavy casualties. Its performance against the Red Army anticipated some of the defects of the IJA as a whole which became apparent during World War Two in the Pacific. A source of constant unrest during the 1930s, the Army remained remarkably obedient during the 1940s, proof to the fact that the Japanese High Command had everything under control - as long as it was willingly to retain it.
Since the outbreak of the Pacific War, many troops were transferred from Manchuria to the Pacific islands. During Operation August Storm, the Soviet Red Army's invasion Japanese-occupied Manchuria in August 1945, the Kantogun's strength was nearly 600,000. The Army by that time was comprised of one armored division, 25 infantry divisions, six independent brigades and up to 25 security battalions. However, much of its heavy weapons and ammunition reserves and best personnel had been transferred to the Pacific and left the Kantogun basically a counterinsurgency and border security force. To cope with the Soviet invasion, the Kantogun planned to form the defence line near Xinjing, which had become the capital of Manchuguo, but Emperor of Japan Hirohito ordered them to surrender before the main defensive engagement took place. At this point, historians relate, little remained of the once-proud and even over-confident Kantogun. Its remnants either lay dead on the battlefield or were on their way to Soviet POW camps. A significant mutiny of the Manchukuo Defence Force also occurred at this time.
The Kantogun was also responsible for the operation of several of Imperial Japan's infamous Biological warfare experimentation program facilities, Unit 100 and Unit 731.