Following this Clayton served in the House of Assembly in the 1778/79 session, and again from the 1780/81 session through the 1783/84 session. He was back again in the 1785/86 session, and the 1787/88 session. He was chosen President of Delaware by the Delaware General Assembly on May 30, 1789 and served as President until January 15, 1793. Under the provisions of the new Delaware Constitution of 1792 he became the first popularly elected Governor of Delaware and continued to serve in that capacity until his term ended, January 19, 1796.