With his battalion, he returned to the United Kingdom in July 1940, ten months after the outbreak of the Second World War, which soon became part of Brigadier Sir Oliver Leese's 29th Independent Infantry Brigade Group. In October he was promoted to the acting rank of brigadier and succeeded Brigadier Evelyn Barker in command of the 10th Infantry Brigade, part of the 4th Infantry Division, stationed in the United Kingdom in Southern England awaiting a German invasion. On 18 November 1941 he was promoted to the general officer rank of acting major-general and became General Officer Commanding of the 1st Infantry Division in succession to Major General Edwin Morris. The division was a Regular Army formation, with a few Territorial Army units, which, like the 4th Division, had fought in France in 1940 and had recently moved to East Anglia, serving under Lieutenant-General Kenneth Anderson's II Corps. On 3 February 1942 Clutterbuck's permanent rank was made colonel. In June 1942 the division was converted into a 'mixed' division of two infantry brigades and one tank brigade, before reverting to a standard infantry division in November. On 18 November, a year after he was made an acting major-general, Clutterbuck's rank of major-general was made temporary, with his permanent rank still being colonel. In late February 1943 the division left the United Kingdom, destined for French North Africa, where, from late April, it was involved in heavy fighting in the final stages of the Tunisian Campaign, mainly under the command of Lieutenant General Charles Allfrey's V Corps, part of Lieutenant General Kenneth Anderson's British First Army until the campaign ended on 13 May. Despite suffering heavy casualties the division earned three Victoria Crosses and captured thousands of Axis soldiers. In mid-June, the division took part in Operation Corkscrew, the Allied invasion of the Italian island of Pantelleria and, despite Clutterbuck's fears that his division would suffer heavy losses, casualties were minimal, with only one man being killed and the Italian garrison of 14,000 surrendered. The division returned to North Africa soon after. However, on 31 July he handed over command of the division, which he had now commanded for over twenty months, to Major General Gerald Templer, who had briefly been his corps commander in England, and returned to the United Kingdom. For his services in North Africa he was awarded the Distinguished Service Order on 5 August. On 15 August he became GOC of the 55th Infantry Division, a first line TA formation. The division was badly understrength, having been reduced to the Lower Establishment in January 1942, and was not fit for active service, although in May 1944 it was raised to the Higher Establishment, and returned to England around the same time. Clutterbuck remained with the division until handing over to Major General Horatio Berney-Ficklin on 13 July 1944.
Postwar
After the war Clutterbuck retired from the army on 18 October 1946, with the honorary rank of major-general. He eventually settled in North Yorkshire, where he farmed, and remained there until his death on 2 February 1987 at the age of 92. He was a local councillor and was Chairman of the Bedale Hunt for many years.