The Supreme Administrative Court of Lithuania was established on 19 September 2000 and started its activities on 1 January 2001. The Court is composed of the President, the Vice-President and other justices. At present, there are 21 justices serving at the Court. Cases at the Supreme Administrative Court are heard by a chamber of three justices, an extended chamber of five or seven justices or a plenary session of the Supreme Administrative Court.

The Supreme Administrative Court of Lithuania, as the supreme judicial institution in administrative cases, develops uniform case law for administrative courts in interpreting and applying laws and other legal acts. Individuals, persons defending public interest and other persons, defending themselves against unlawful actions of state authorities (officials), usually first apply to courts of the first instance, the decisions of which may then be appealed against the Supreme Administrative Court of Lithuania. Rulings of the Supreme Administrative Court of Lithuania are final and not subject to appeal. The Supreme Administrative Court is also the first and final instance for certain categories of administrative cases assigned to its jurisdiction by law. According to the Law on Administrative Proceedings, it hears petitions on the reopening of proceedings in administrative cases ended by res judicata court judgements, investigates requests by entities of municipal administration to present conclusions about whether a member of municipal administration has broken an oath, as well as requests by State Data Protection Inspectorate to address EU judicial authority where European Commission decision is in doubt. Furthermore, resolution of disputes concerning breaches of the laws on election or referendum is also assigned to the jurisdiction of administrative courts. Persons specified in the Law on Presidential Elections, the Law on Elections to the Seimas, the Law on Referendum and the Law on Elections to Municipal Councils are entitled to file petitions concerning decisions of the Central Electoral Commission directly to the Supreme Administrative Court of Lithuania.

Certain individuals may apply directly to the Supreme Administrative Court of Lithuania in particular cases prescribed by law. For example, members of the Parliament of the Republic of Lithuania (the Seimas), courts, the Seimas Ombudsperson, the Ombudsperson for Children Rights, the Equal Opportunities Ombudsperson, the professional self-governance associations established by law to carry out public functions and prosecutors for the state are entitled to challenge the legitimacy of regulatory administrative enactment passed by central entities of state administration as well as legitimacy of general acts adopted by societies, political parties, political organisations or associations by applying directly to the Supreme Administrative Court of Lithuania.