The Supreme Court was established under the Federation of Malaya Agreement in 1948.

The Supreme Court was then replaced with the Federal Court and three other High Courts namely, the High Court of Malaya, the High Court of Singapore, and the High Court of Borneo. On the 9th of August 1965, Singapore decided to be separated om Malaysia. Therefore, only the High" Court of Malaya and the High Court of Borneo were retained.

On the 1st of January 1985, the Federal Court was renamed as the Supreme Court under the Constitution (Amendment) Act 1983 In parallel with such amendment, Article 131 which allowed the appeals from the Federal Court to be referred to the Privy Council was abolished. The repeal of the aforesaid article indicates that the appeal process to the Privy Council has ended. The abolition of Article 131 means that the existing two-tier process of appeal has been changed into one tier process only.

In 1994, the Supreme Court was renamed to the Federal Court again made under the amendment of the Federal Constitution on the 24th of June 1994. The title of Lord President has also been changed to the Chief Justice.