Born in Mount Vernon, Illinois, Thomas attended the common schools and Hunter Collegiate Institute, Princeton, Indiana.

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.

The conservative "Stalwart" faction of the Republican Party which earlier opposed civil service reform almost entirely voted for the Pendleton Act under immense political pressure following the assassination of James A. Garfield.

[2] According to an account by J. Stanley Clark that appeared in the Chronicles of Oklahoma in 1974, Judge Thomas had gone to the penitentiary to interview Abraham Collier, who was serving a seven-year sentence for larceny.

Following the possession of a gun by three prisoners, they took keys to unlock themselves from their confinement spaces and barged into offices to use stenographer Mary Foster as a human shield.

Their daughter, Carolyn, who married Grant Foreman, was an author and historian who wrote several books about Native Americans and the history of Oklahoma.

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.