The Judiciary Act of 1789 established a system of federal courts that extended throughout the nation, but the statute created no central agency to provide for the courts' collective administrative and budgetary needs. For 150 years, the administrative responsibility for the courts shifted between executive branch departments. In the twentieth century, the Congress established independent administrative agencies for the third branch of government and instituted a more formal separation of powers. Each of the following departments or agencies has played a significant role in the administration of the federal judiciary.

Department of the Treasury, 1789-1849
From the inauguration of the federal government in 1789 until 1849, the Treasury Department supervised the financial administration of the federal courts. The act establishing the Treasury Department in September 1789 gave it responsibility for disbursing all appropriated money from the federal Treasury and for receipt of all revenues of the United States, thus connecting it to the daily operation of federal courts as well as executive branch officials such as customs officers throughout the nation. Further legislative mandates required all federal officials receiving public money to submit proper accounts. Congress specifically instructed clerks of the federal courts to submit to the Department of the Treasury, within 30 days of the adjournment of a court session, a list of all judgments and decrees to which the United States was a party, with the monetary amounts awarded for and against the federal government. Until 1849, the courts' accounts with the Department of the Treasury provided the only central record of the business before the lower courts of the United States.

Department of State, 1789-1888
As a kind of home office as well as an office of foreign affairs, the Department of State was responsible for several aspects of judicial administration during the first century of the federal government. According to an act of September 1789, Congress charged the Department of State with responsibility for the great seal of the United States, which was to be affixed to all civil commissions approved by the president. The department issued the commissions, including those which authorized newly appointed judges to take the oath of office and hold court, and maintained records of judges' commissions until Congress transferred responsibility for judicial appointments to the Department of Justice in 1888. The early courts also relied on the Department of State to distribute printed compendiums of public statutes. In practice, the secretary of state played the principal role in advising the president on judicial nominations in the early years of the government, and, although the attorney general informally assumed this responsibility beginning in the 1850s, the Department of State maintained the records of judicial nominations throughout the nineteenth century.

Department of the Interior, 1849-1870
In 1849, "An Act to establish the Home Department ... to be called the Department of the Interior" created a new cabinet department that assumed oversight of the financial administration of the federal courts. The act transferred from the Department of the Treasury to the Department of the Interior responsibility for the supervision of the accounts of all officers of the federal courts. Henceforth, clerks, marshals, and district attorneys submitted to the Department of the Interior all accounts of fees received by their respective courts and all requisitions for the advance or payment of federal money. Interior Department officials regularly corresponded with court officers about many aspects of the operation of the federal courts, including the rental and furnishing of court buildings, travel expenses of judges and court officers, and salary disbursal. The Department of the Interior closely supervised the financial management of each federal court and enforced spending regulations.

Department of Justice, 1870-1939
According to the act establishing the Department of Justice in 1870, the attorney general, as head of the department, assumed the "supervisory powers now exercised by the Secretary of the Interior over the accounts of the district attorneys, marshals, clerks, and other officers of the courts of the United States." In August 1888, Congress also transferred to the Department of Justice the State Department's responsibility for the issuance of commissions for all judicial officers, including judges, marshals, and U.S. attorneys. In addition to its supervision of the courts' financial accounts and preparation of budget requests, the Department of Justice until 1939 served as the principal administrative agency for the judiciary, compiling statistics on the business of the federal courts, procuring office supplies, and developing more uniform standards of personnel management. The appropriations for the federal courts were included in the legislation funding the Department of Justice.