Thomas served as the 11th Governor of Colorado from 1899 to 1901. In 1897, Colorado had abolished the death penalty, but Thomas considered lynching an understandable substitute. In 1900, when a lynch mob murdered Calvin Kimblern, Thomas called it "a natural outburst of indignation of the people of Pueblo" and blamed the lack of a death penalty for the murder.[2] Six months later, a mob surrounded Denver's jail seeking to lynch 15-year-old Preston Porter. Thomas was informed but declined to intervene. "As a matter of fact, hanging is too good for that man," he told reporters. The spirit of the lynch law is with the people, and will remain in them just as long as the Anglo-Saxon exists."[3] After Porter was burned alive by a mob, when Thomas was asked to comment on the lynching, he said, "My opinion is that there is one less negro in the world."[4] Colorado reinstated the death penalty soon thereafter.[2]
In 1913, Thomas was elected as a Democrat to the United States Senate in 1912 to fill the vacancy caused by the death of Charles J. Hughes, Jr.; in 1914, he was narrowly reelected to a full term in the face of split opposition. Thomas served from January 15, 1913, to March 3, 1921, and was the last Confederate veteran to serve in the Senate.[5] In 1920, he was an unsuccessful candidate for reelection on the Nationalist ticket, receiving only 3% of the vote.[6]
In the Sixty-third and Sixty-fourth Congresses, Thomas was chairman of the Committee on Woman Suffrage, and a member of the Committee on Coast Defenses (Sixty-fifth Congress) and the Committee on Pacific Railroads (Sixty-sixth Congress). He resumed the practice of law in Denver, where he died on June 24, 1934; his remains were cremated and his ashes were scattered in the mountains.