The initial supreme commander of the theatre was General Sir Archibald Wavell while head of the short-lived American-British-Dutch-Australian Command which was dissolved after the fall of Singapore and the Dutch East Indies. In August 1943, the Allies created the combined South East Asian Command, to assume overall strategic command of all air, sea and land operations of all national contingents in the theatre. In August 1943, with the agreement of the Combined Chiefs of Staff, Winston Churchill appointed Admiral Lord Louis Mountbatten as Supreme Allied Commander South East Asia, a post he held until 1946. The American General Joseph Stilwell was the first deputy supreme Allied commander, as well as heading the U.S. China Burma India Theater (CBI) command. Mountbatten arrived in India on 7 October and SEAC came formally into being in Delhi at midnight 15–16 November. The headquarters moved in April 1944 to Kandy in Ceylon.
On 2 December 1943 the Combined Chiefs of Staff approved in principle a staff plan designating the main effort against Japan to be the Pacific as the most rapid means of coming in range of the home islands for aerial bombardment. The secondary advance was "along the New Guinea-N.E.I.-Philippine axis" under the South West Pacific Area Command. The South East Asia theatre, along with the North Pacific, the South Pacific and China efforts were designated to be supportive. At that time available forces were seen to be limited due to British commitment against Germany with major advances not anticipated until autumn of 1944 and after the defeat of Germany. The focus on the Central Pacific and South West Pacific were a compromise reached at the Casablanca Conference in which British views focused on the war against Germany with the entire war against Japan being limited "to the defense of a fixed line in front of those positions that must be held"—an approach unacceptable to the United States. Offensive actions in Burma, support of China and other theatre activity beyond holding a defensive line in South East Asia, the position of the British Chiefs, were the result of American demands that the Japanese be kept off balance throughout areas of Allied/Japanese contact.
The initial land forces operational area for SEAC was India, Burma, Ceylon, Malaya, northern islands of Sumatra, and, for offensive operations, Siam (Thailand). On 15 August 1945 this was expanded to include the rest parts of Dutch East Indies and southern part of French Indochina.
Command arrangements in SEAC were always complicated. Ideally there should have been under the Supreme Commander a Commander in Chief for each of the land sea and air forces. This was implemented for the naval and air forces but the British 11th Army Group, under SEAC itself, controlled only British forces. US and Chinese forces serving in the South East Asian theatre, organised as the Northern Combat Area Command or NCAC commanded by Stilwell, answered directly to the Supreme Commander because Stilwell refused to serve under the 11th Army Group commander George Giffard. The Eleventh Army Group had the Fourteenth Army on the Burma front, and the British garrison in Ceylon under its direct command. Stilwell also served as Chief of Staff to Chiang Kai-shek, who was officially the Supreme Allied Commander in China. Air Chief Marshal Sir Richard Peirse was appointed the Air Commander in Chief under Mountbatten. Air units taking part in the Burma Campaign were, at first, part of either the RAF Third Tactical Air Force or the USAAF Tenth Air Force. Tenth Air Force came under SEAC only through Stilwell as commanding General CBI Theater. To avoid a potentially cumbersome chain of command and overlapping effort Mountbatten gave orders in December for the two air forces to be integrated under the name Eastern Air Command. The US Fourteenth Air Force, which was based in China and the US Twentieth Air Force – strategic bomber units based in India – were never controlled by SEAC but their operations were coordinated with SEAC. At sea, the command structure was relatively simple, since the Royal Navy was providing almost all naval forces in the area. Admiral Sir James Somerville, Commander-in-Chief, Eastern Fleet, became the naval commander under Mountbatten.
It was not until late 1944 that the land forces chain of command was clarified, after Stilwell was recalled to Washington. His overall role, and the CBI command were then split among three people: Lt Gen. Raymond Wheeler became Deputy Supreme Allied Commander South East Asia; Maj. Gen. Albert Wedemeyer became Chief of Staff to Chiang, and commander of US Forces, China Theater (USFCT). Lt Gen. Daniel Sultan was promoted, from deputy commander of CBI to commander of US Forces, India-Burma Theater (USFIBT) and commander of the NCAC. The 11th Army Group was redesignated Allied Land Forces South East Asia (ALFSEA) under a new commander Lieutenant-General Oliver Leese who had relinquished command of the Eighth Army in Italy, and NCAC (which by this time included Chinese, American and British units) was placed under ALFSEA. As the drive to liberate Burma began in earnest however, Chiang Kai-shek and Wedemeyer made increasing demands for NCAC's formations to be moved to the China Theatre to meet the threat of Japanese attacks from the north. Once the Burma Road from Mandalay to Chungking was secured NCAC became passive and in March 1945 Mountbatten agreed to the US and Chinese troops in NCAC being gradually withdrawn to the China.