After returning to Australia, Wilton was appointed Brigadier in Charge of Administration at Headquarters Eastern Command, his first administrative post. In November 1955 he was assigned to the General Staff at AHQ, where he was responsible for intelligence, operations and plans, and took part in Australian preparations for SEATO exercises. He was promoted to major general on 24 March 1957, and became Commandant of the Royal Military College, Duntroon. Although not strongly religious, Wilton considered himself responsible for the spiritual and moral development of younger cadets; he made a point of attending church parade regularly, and in 1959 personally launched an appeal for public funds to build the college's Anzac Memorial Chapel, which would open in 1966. His chief goal, though, was academic: concerned that graduates were at risk of falling behind their increasingly tertiary-qualified peers in industry and public service, he worked assiduously to make the college a degree-granting institution; this was realised in 1967. From June 1960 through 1962, Wilton was Chief of the Military Planning Office at SEATO Headquarters, Bangkok. He believed Thailand to be strategically vital, declaring "if you want to hold Southeast Asia, you need to hold Thailand". His position allowed him to closely observe the deteriorating situation in Laos, which threatened to spill over into Thailand, and the Western Powers' growing focus on South Vietnam. He was appointed a Companion of the Order of the Bath (CB) in the 1962 Queen's Birthday Honours, in particular for his "conspicuous devotion to duty and his singleness of purpose" as Commandant of Duntroon. On 21 January 1963, Wilton was promoted lieutenant general and became Chief of the General Staff (CGS), succeeding Lieutenant General Sir Reginald Pollard. He was appointed a Knight Commander of the Order of the British Empire (KBE) in the 1964 New Year Honours.