The Azad Kashmir provisional government took control of the force by sending Colonel Aslam Khan as its commander.

When the Gilgit Agency was established in 1889, it was controlled using the Imperial Service Troops provided by the Maharaja of Jammu and Kashmir and placed under the command of the British Political Agent.

[5] After the Hunza–Nagar Campaign in 1891, and the pacification of Chilas and Chitral, the British Indian troops were gradually reduced, and replaced by new levies from Hunza, Nagar and Punial.

Historian Ahmad Hasan Dani, a member of the Shina community which is the majority ethno-linguistic group of the Gilgit Baltistan region of Pakistan,[10] mentions that although there was lack of public participation in the rebellion, pro-Pakistan sentiments were intense in the civilian population and their anti-Kashmiri sentiments were also clear.

[11] On 2 November, the Pakistani flag was raised on the old tower in the Gilgit Scout Lines, under the command of Major Brown.

[12] After the conclusion of the First Kashmir War, the Gilgit Scouts operated as a paramilitary force in the Northern Areas (now called Gilgit-Baltistan).