Thornton was appointed as a Democrat to the U.S. Senate on August 27, 1910, and was subsequently elected to fill the vacancy caused by the death of Samuel D. McEnery, serving from December 7, 1910, to March 3, 1915; he was not a candidate for reelection to the Senate. While in the Senate he was chairman of the Committee on Fisheries (Sixty-third Congress).
On August 27, 1910, Thornton was appointed as a Democrat to the U.S. Senate and later elected to fill a vacancy caused by Samuel D. McEnery's death, serving from December 7, 1910, until March 3, 1915; he did not seek re-election for the Senate. While in the Senate, he chaired the Committee on Fisheries (Sixty-third Congress).