Educated in Scotland as a physician, Thornton rarely practiced his profession. He was a self-taught architect, painter, and inventor. His
design for the Capitol, submitted after the competition of 1792 had closed, was approved by President Washington, who praised it for its "grandeur, simplicity and convenience." A prize of $500 and a city lot was awarded to Thornton on April 5, 1793; he is thus recognized as the first Architect of the Capitol.
On September 12, 1794, the President appointed Thornton one of the three Commissioners of the Federal District in charge of laying out the new federal city and overseeing construction of the first government buildings, including the Capitol. Upon the abolition of the board in 1802, President Jefferson appointed Thornton Superintendent of the Patent Office, a position which he held until his death.
Three professional architects supervised the construction of the north wing of the Capitol from Thornton's design: Stephen Hallet (1793-94); George Hadfield (1795-98); and James Hoban (1798-1800).