In April 1939, during the build-up to the Second World War, John Anderson, the Home Secretary, appointed Johnston as Commissioner for Civil Defence in Scotland. In this role, Johnston oversaw preparations for aerial bombardment and possible invasion, and the organisation of shelter and relief work. Prime Minister Winston Churchill appointed Johnston as Secretary of State for Scotland on 12 February 1941, and Johnston retained the post until May 1945. As Devine (1999) concludes, "Johnston was a giant figure in Scottish politics and is revered to this day as the greatest Scottish Secretary of the century...In essence, Johnston was promised the powers of a benign dictator.".