In pursuance of a Judgment of the Supreme Court of Pakistan in the case Al-Jehad Trust Versus Federation of Pakistan etc. reported in 1999 SCMR, Page 1379, Government of Pakistan established Northern Areas Court of Appeals at Gilgit vide Gazette of Pakistan, extraordinary, part II dated 8 November 1999 with Appellate Jurisdiction, the Court started function on 27 September 2005, when the Chairmen and members were appointed. on 15 December 2007 by virtue of amendments in the Northern Areas Governance order 1994, the nomenclature of the Court was re-designated as Northern Areas Supreme Appellate Court and its jurisdiction was also enlarged by conferring Original and Appellate jurisdiction, It was also given the Status equal to the Supreme Court of Azad Jammu and Kashmir.
On 9 September 2009, the Supreme Appellate Court was conferred the similar jurisdiction equal to the Supreme Court of Pakistan by promulgating Gilgit-Baltistan ( Empowerment and Self Governance Order) 2009. Now under the Government of Gilgit-Baltistan Order, 2018 almost the same jurisdiction of Supreme Appellate Court is maintained. The Supreme Appellate Court has its own rules of procedure of 2008.
The Supreme Appellate Court is consisting of a Chief Judge and two Judges. The Permanent Seat of the Court is at Gilgit, but the Court also sits from time to time at Skardu Branch Registry.