After the 1895 general election, Selborne, now sitting in the Lords, was appointed Under-Secretary of State for the Colonies by his father-in-law Lord Salisbury, where he became junior to the Colonial Secretary Joseph Chamberlain. During the difficult period before the outbreak of the Second Boer War he progressed rapidly. In November 1900 Selborne was sworn of the Privy Council and made First Lord of the Admiralty under Salisbury, with a seat in the cabinet, an office he retained when Arthur Balfour became Prime Minister in 1902. In 1905 he succeeded Lord Milner as High Commissioner for Southern Africa and governor of the Transvaal and Orange River colonies. He assumed office at Pretoria in May of that year. He had gone out with the intention of guiding the destinies of South Africa during a period when the ex-Boer republics would be in a transitional state between crown colony government and self-government, and letters patent were issued granting the Transvaal representative institutions.
