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The Office of the State Auditor has its derivation through the State Bank Examiner who was appointed by the Governor with the advice of the South Carolina Bankers' Association. In addition to his bank examination duties, he had the additional duty of examining the records of all state and county offices charged with the receipt and disbursement of public funds as well as the records of those state, educational, charitable and correctional institutions for whose support the state contributed an appropriation or made a provision of law.

In 1933, the Code of Laws abolished the Office of the State Bank Examiner and provided the appointment of the State Auditor. Previous duties associated with the State Bank Examiner were transferred to the Budget Committee whose membership was comprised of the Governor, the Chairman of the Senate Finance Committee, and the Chairman of the House Ways and Means Committee. The Budget Committee selected the State Auditor who in turn chose his assistants.

With the creation of the State Budget and Control Board, the Office of the State Auditor, the Budget Commission, State Finance Committee and the Board of Claims were combined into one organization called the Finance Division whose director was the State Auditor. During Fiscal Year 1983-84, the Finance Division was reorganized by the Budget and Control Board, and on January 1, 1984, the Office of the State Auditor began operating as a separate entity without the budgetary function.

The South Carolina Restructuring Act of 2014 (Act 121) eliminated the Budget and Control Board on June 30, 2015.  Act 121 created the State Fiscal Accountability Authority.  The Authority is governed by the Governor, State Treasurer, Comptroller General, Chairman of the House Ways and Means Committee, and the Chairman of the Senate Finance Committee.  Effective July 1, 2015, the Office of the State Auditor was transferred to, and incorporated into, the State Fiscal Accountability Authority.

The State Auditor reports directly to five members of the Authority.