One of the first acts passed in the newly formed Czechoslovak Republic was Act No. 5/1918 Sb, which established the Supreme Court and defined its status. Originally seated in Prague, the Supreme Court was moved to Brno in 1919. The Supreme Court was the third instance for both civil and criminal matters. In addition, it could make suggestions for the adoption of Acts of Parliament relating to justice, as well as amendments thereto. Its structure was almost identical to that of the Supreme Court of Justice and Cassation in Vienna, as it functioned until 1918. The Supreme Court consisted of a first and a second president, seven bench presidents (nine presidents after 1930) and forty council members (forty-eight council members after 1930).

As a result of the creation of the Protectorate, after 1945 there were two Supreme Courts, as the Slovak Supreme Court (established in 1939 and seated in Bratislava) was added to the original First Republic Supreme Court. In 1945 and 1946, the government of Czechoslovakia made an agreement with the Slovak National Council that, while both supreme courts in Brno and Bratislava would be maintained with their structure and jurisdiction according to the then current legislation, they would be considered as forming part of a unitary Supreme Court, seated in Brno.

The 1948 Act on the Popularization of the Judiciary significantly affected the Supreme Court, as its composition was supplemented by appointing the required number of lay judges. Senates consisted of two professional judges and three observing lay judges. Lay and professional judges had an equal vote in the decision-making process. The lay judges even took part in decisions on complaints of the violation of the law. In view of the fact that lay judges were appointed by the government, the principles of impartiality and independence were seriously violated.

On the basis of the Constitutional Act on Czechoslovak Federation, in 1968 a structure of federal authorities arose. Alongside the Supreme Court of the Czechoslovak federation, Supreme Courts were also established in both republics. The Supreme Court of the Czechoslovak Socialist Republic was the highest judicial organ for the entire federation and had its seat in Prague. Its main task was to supervise the legality of court decisions and to ensure unified judicial decision-making. The sphere of its activity was practically identical to that presently existing, except that the Supreme Court was never used as a court of first instance. A specific example was the examination of the legality of final decisions, in which capital punishment was imposed. By that time, the three or five member senates were made up solely of professional judges. There were three Collegia: civil, criminal and martial.

There have been fundamental changes in the entire legal system following the events of 1989. These have affected the Supreme Court predominantly in the area of personnel; the Court's organizational structure and status have remained unchanged. The basic change came with the split of the Czech and Slovak Federal Republic. The system of federal and republic organs was abolished, and from 1993 there has been a unitary judicial organization. The competencies belonging to the Supreme Court of the Czech and Slovak Federal Republic were passed to the Supreme Court of the Czech Republic on 1st January 1993.