Formed in mid-1942 as part of defensive measures to protect the eastern coast of Australia from invasion, the corps was initially composed mainly of home defence troops drawn from the Militia.

After the threat of invasion passed, the corps took more of an operational role and from late 1943 until the end of the war it commanded a mix of Second Australian Imperial Force and Militia units in action against the Japanese in New Guinea and on Bougainville.

By August 1943, II Corps was under the command of Lieutenant General Leslie Morshead, with its headquarters at Barinne, with the 6th Division (consisting of the 16th and 19th Infantry Brigades), and the 2/7th Cavalry Commando Regiment under its control.

Meanwhile, advanced elements of II Corps headquarters moved from Finschhafen, leaving a rear detachment behind at Dobodura.

In April, Madang was captured, effectively bringing large scale combat operations to a close temporarily for Australian forces in New Guinea, and allowing a reorganisation.

[10] The final months of 1944 saw the Australians assume responsibility for several rear areas in New Guinea and elsewhere, to relieve US troops and free them up for further offensives in the Philippines.

Consequently, the 5th Division became a direct command unit of the First Army for its deployment to New Britain,[12] and Headquarters New Guinea force was redesignated as II Corps in September.

II Corps subsequently moved to Torokina, on Bougainville, in November to take over from the US XIV Corps,[13] and to direct the operations of the 3rd Division (consisting of the 7th, 15th and 29th Infantry Brigades), as well as two other brigades – 11th and 23rd, with the later initially detailed to defend the Outer Islands (Green, Emirau, and the Treasury Islands, and Munda, on New Georgia).

As preparations were made for the post-war draw down of Australia's military, the 23rd Brigade was chosen to remain on Bougainville as a garrison force.