In 1899, Clarke found himself in total disagreement with his party over the government's South African policy, and in early February 1900 his constituency party in Plymouth called upon him to resign his seat. He resigned the following day. He did not contest the general election of 1900, but returned to the House as MP for the City of London in 1906; however, he offended a section of his constituents by a speech against tariff reform in the House of Commons on 12 March 1906, and shortly afterwards he resigned his seat again on grounds of health.