Cooper entered the gubernatorial election of 1918 and won the general election without opposition to become the 93rd governor of South Carolina. He continued the progressive policies of his predecessor, Richard Irvine Manning III, by establishing a seven-month school term, mandating compulsory school attendance, expanding health care, and improving the state roadways. These initiatives were paid for by stricter enforcement of existing tax laws and re-evaluating state property. Cooper was elected to a second term in 1920.
He resigned from the governorship in 1922 to accept an appointment to the Federal Farm Loan Board that lasted five years. After this, Cooper returned to the practice of law but was called by President Franklin D. Roosevelt to serve as the General Counsel of the Commodity Credit Corporation. Roosevelt later appointed him in 1934 as Judge of the District Court for Puerto Rico, a position Cooper held until 1947. Cooper died on August 7, 1953, and was buried at the Laurens City Cemetery in Laurens.
Guillermo A. Baralt, History of the Federal Court in Puerto Rico: 1899-1999 (2004) (also published in Spanish as Historia del Tribunal Federal de Puerto Rico)