The Court of Tax Appeals was originally created by virtue of Republic Act. No. 1125 which was enacted on June 16, 1954 and was recently amended by Republic Act. No. 9282 on March 30, 2004, which took effect on April 23, 2004. Under Section 1 of the new law, the Court is headed by a Presiding Justice and assisted by five (5) Associate Justices. They shall have the same qualifications, rank, category, salary, emoluments and other privileges, be subject to the same inhibitions and disqualifications and enjoy the same retirement and other benefits as those provided for under existing laws for the Presiding Justice and Associate Justices of the Court of Appeals.

Previously, only decision, judgment, ruling or inaction of the Commissioner of Internal Revenue, the Commissioner of Customs, the Secretary of Finance, the Secretary of Trade and Industry, or the Secretary of Agriculture, involving the National Internal Revenue Code and the Tariff and Customs Code on civil matters are appeallable to the Court of Tax Appeals. The expanded jurisdiction transferred to the CTA the jurisdiction of the Regional Trial Courts and the Court of Appeals over matters involving criminal violation and collection of revenues under the National Internal Revenue Code and Tariff and Customs Code. In addition, it also acquired jurisdiction over cases involving local and real property taxes which used to be with the Regional Trial Court and the Court of Appeals.