Prior to 1972, no regular Courts like the other parts of the country had been functioning in Gilgit Baltistan and judicial matters were dealt under the FCR. The Resident Commissioner was exercising the powers of a Judge of High Court; the Political Agent was vested with the powers of District & Sessions Judge while the Assistant Political Agents were functioning as Civil Judges. In 1972 some sort of administrative and judicial system had introduced over the area by abolishing FCR and the laws of Pakistan also extended to Gilgit-Baltistan by the Kashmir Affairs Ministry, consequently Gilgit-Baltistan was declared one Sessions division by appointing a District and Sessions Judge at Gilgit and Civil Courts were also established.

The Court of Resident Commissioner exercising the same powers of Judge High Court was substituted with the Court of Judicial Commissioner in 1976 with the powers of High Court and another Court of District and Sessions Judge was also established in Skardu. Later on some other posts of District and Sessions Judges were created in the newly established districts in the Northern Areas.The most senior District & Sessions Judges of NWFP Judiciary were appointed as Judicial Commissioners Northern Areas.

The following Judges served as Judicial Commissioners in the Northern Areas.

Mr. Shafi Mohammad R. Akhund

From 25-03-1976 to 01-09-1976

Mr. Shafi Mohammad R. Akhund

From 25-03-1976 to 01-09-1976

Mr. Mohammad Bashir Jehangiri

From 26-06-1979 to 12-12-1982 (Elevated as Judge in Peshawar High Court, elevated as Judge in Supreme Court of Pakistan and retired as Chief Justice of Pakistan).

Mr. Mahbub Ali Khan

From 22-03-1983 to 25-07-1984 (Elevated as Judge in Peshawar High Court).

Mr. Sardar Muhammad Raza

From 26-07-1984 to 08-10-1988 (Elevated as Judge in Peshawar High Court, elevated as Judge in Supreme Court of Pakistan and retired as Judge, now functioning as Chief Election Commissioner of Pakistan).

Mr. Muhammad Nawaz Khan

From 09-10-1988 to 29-05-1990

Syed Ijaz-ul-Hassan

From 23-06-1990 to 08-08-1992 (Elevated as Judge in Peshawar High Court).

Mr. Muhammad Khurshid Khan

From 09-11-1992 to 01-08-1993 (on current charge basis)

Mr. Muzaffar-H-Malik

From 02-08-1993 to 23-11-1994 (on current charge basis)

In the year 1994, the Federal Government further introduced reforms in judicial system and the Court of Judicial commissioner Northern Areas was converted into Chief Court under the Chief Court Establishment Order 1998, which was comprised of a Chairman and two Members, with the same judicial powers as were vested to the Judicial Commissioner.

The following Judges served as Chairman Chief Court:

Mr. Justice Muhammad Ishaq Khan

From 24-11-1994 to 09-08-1998

Mr. Justice Zeenat Khan

From 10-08-1998 to 24-10-2000

Mr. Justice Muzaffar-H-Malik

From 27-10-2000 to 04-02-2004

Mr. Justice Muhammad Khurshid Khan

From 05-02-2004 to 13-11-2004 (on acting charge basis)

Mr. Justice Raja Jalal Uddin

From 23-11-2004 to 29-04-2005 (on acting charge basis)

Mr. Justice Raja Jalal Uddin

From 30-04-2005 to 08-09-2009

When the August Supreme Court of Pakistan pronounced its land mark judgment in case titled "Al-Jehad Trust Versus Federation of Pakistan" reported in 1999 SCMR 1379 and ordered Federation of Pakistan to equate the Chief Court with High Court and also conferred the writ jurisdiction for the enforcement of the fundamental rights of Northern Areas with in a period of six months by declaring the people of Northern Areas as citizens of Pakistan. The Government of Pakistan empowered the Chief Court to entertain the writ petitions by implementing the judgment of the Apex Court of Pakistan through amendments in the Northern Areas Governance Order 1994 in the month of October/November 1999.

In 2007, the Federal Government conferred more powers to the Chief Court and it was brought at par with the other Provincial High Courts and the designation of Chairman was substituted with Chief Judge, whereas the members were named as Judges, later on their perks and privileges were also brought at par with the Chief Justice and Judges of Provincial High Courts like other Provinces of Pakistan. In the year 2009, the Government of Pakistan promulgated Gilgit-Baltistan (Empowerment and Self Governance) Order, 2009, in Gilgit-Baltistan and through the said Order a Provincial set-up was given to the area. The strength of Judges of Chief Court was increased from three to five.

The following Hon’ble Judges served/serving as Chief Judge Gilgit-Baltistan Chief Court.

Mr. Justice Raja Jalal Uddin

From 09-09-2009 to 07-02-2013

Mr. Justice Sahib Khan

From 08-02-2013 to 10.06.2017

Mr. Justice Wazir Shakeel Ahmed (Acting Chief Judge)

From 12-06-2017 30.11.2017.

Mr. Justice Wazir Shakeel Ahmed (Chief Justice)

From 30-11-2017 to 31.01.2020.

Mr. Justice Malik Haq Nawaz (Chief Justice)

From 31-01-2020 to 28-08-2021.

Mr. Justice Ali Baig (Acting Chief Justice)

From 01-09-2021 15-09-2021.

Mr. Justice Ali Baig (Chief Justice)

From 16-09-2021 to till now.