The Japanese 16th Army was formed on November 5, 1941, under the Southern Expeditionary Army Group to coordinate the infantry divisions and other Japanese ground forces in the Invasion of Java in the Netherlands East Indies.

It remained based on Java throughout the Pacific War as a garrison force.

On March 27, 1944, with the threat of possible landings of Allied forces to retake the Dutch East Indies increasing, the organizational structure of the Southern Expeditionary Army changed and the IJA 16th Army was reassigned to the Japanese Seventh Area Army.

It remained headquartered in Jakarta as a garrison force as before.

The Japanese 16th Army was demobilized at the surrender of Japan on August 15, 1945.