After nine years in opposition and academia, Smuts returned as Deputy Prime Minister in a 'grand coalition' government under Barry Hertzog. When Hertzog advocated neutrality towards Nazi Germany in 1939, he was deposed by a party caucus, and Smuts became Prime Minister for the second time. He had served with Winston Churchill in World War I, and had developed a personal and professional rapport. Smuts was invited to the Imperial War Cabinet in 1939 as the most senior South African in favour of war. On 28 May 1941 Smuts was appointed a field marshal of the British Army, becoming the first South African to hold that rank.

Smuts' importance to the Imperial war effort was emphasised by a quite audacious plan, proposed as early as 1940, to appoint Smuts as Prime Minister of the United Kingdom, should Churchill die or otherwise become incapacitated during the war. This idea was put by Sir John Colville, Churchill's private secretary, to Queen Mary and then to George VI, both of whom warmed to the idea. As Churchill lived for another twenty-five years, the plan was never put into effect and its constitutionality was never tested. This closeness to the British establishment, to the King, and to Churchill made Smuts very unpopular amongst the Afrikaners, leading to his eventual downfall.


In May 1945, he represented South Africa in San Francisco at the drafting of the United Nations Charter. Just as he did in 1919, Smuts urged the delegates to create a powerful international body to preserve peace; he was determined that, unlike the League of Nations, the United Nations would have teeth. Smuts signed the Paris Peace Treaty, resolving the peace in Europe, thus becoming the only signatory of both the treaty ending the First World War, and that ending the Second.