Born in Mount Vernon, Illinois, Thomas attended the common schools and Hunter Collegiate Institute, Princeton, Indiana. He studied law and was admitted to the bar in 1869.
He served in the Union Army during the Civil War, and rose from the rank of private to that of captain of Company D, One Hundred and Twentieth Regiment, Indiana Volunteer Infantry. He became city attorney of Metropolis, Illinois, 1869 and 1870 and served as State's attorney 1871-1874. Thomas was elected as a Republican to the Forty-sixth and to the four succeeding Congresses (March 4, 1879-March 3, 1889).
He served as chairman of the Committee on Levees and Improvements of the Mississippi River (Forty-seventh Congress). He was not a candidate for renomination in 1888. He resumed the practice of law in Muskogee, Oklahoma, and also served as a United States judge in the Indian Territory from June 30, 1897, to June 30, 1901.
He was nominated for judge of the supreme court by the first Republican State convention of Oklahoma, but declined the nomination. He died in McAlester, Oklahoma, January 19, 1914, and was interred in Green Hill Cemetery, Muskogee, Oklahoma. He was reinterred in Arlington National Cemetery.
He was the son of Major William Allen Thomas and Caroline (Neely) Thomas. A daughter, Carolyn, who married Grant Foreman, was an author and historian who wrote several books about Native Americans and the history of Oklahoma. A son, John R. Thomas Jr., was a "celebrated hero of the Spanish-American War with the Rough Riders." Thomas-Foreman Historic Home In 1884, while serving as US Congressman, John Robert Thomas was also Grand Master for the Ancient Free and Accepted Masons of the State of Illinois.
He served as member of the Oklahoma State Code Commission 1908-1910.