Upon the abolition of the board in 1802, President Jefferson appointed Thornton the first Superintendent of the Patent Office. When Washington was burned by the British in 1814, Thornton convinced them not to burn the Patent Office because of its importance to mankind. He held the position from June 1, 1802 until his death in 1828 in Washington, DC. During his tenure, he introduced innovations including the patent reissue practice, which survives to this day.