Before the independence of Pakistan and the partition of India in 1947, Maharaja Hari Singh extended his rule to Gilgit and Baltistan. After the partition, Jammu and Kashmir, in its entirety, remained an independent state. The Pakistani parts of Kashmir to the north and west of the cease-fire line established at the end of the Indo-Pakistani War of 1947, or the Line of Control as it later came to be called, were divided into the Northern Areas (72,971 km²) in the north and the Pakistani state of Azad Kashmir (13,297 km²) in the south. The name "Northern Areas" was first used by the United Nations to refer to the northern areas of Kashmir. A small part of the Northern Areas, the Shaksgam tract, was provisionally ceded by Pakistan to the People's Republic of China in 1963.

Gilgit-Baltistan, which was most recently known as the Northern Areas, presently consists of seven districts, has a population approaching one million, has an area of approximately 28,000 square miles, and shares borders with Pakistan, China, Afghanistan, and India. The people of this remote region were liberated from the Dogra regime of the former princely state of Jammu and Kashmir on 1 November 1947 without any external assistance and then became citizens of a self-liberated and very short-lived independent state. The new state asked the government of Pakistan to provide it with necessary assistance with which to conduct its affairs, as it did not have the necessary administrative infrastructure of its own. The government of Pakistan accepted the request and sent Sardar Muhammad Alam Khan, an extra assistant commissioner from the NWFP, to Gilgit. Sardar Muhammad Alam Khan then took control of the territory's administration as its first appointed political agent.

The local Northern Light Infantry is the army unit that was believed to have assisted and possibly participated in the 1999 Kargil conflict. More than 500 soldiers were believed to have been killed and buried in the Northern Areas in that action.[6] Lalak Jan, a soldier from Yasin Valley, was awarded Pakistan's most prestigious medal, the Nishan-e-Haider, for his courageous actions during the Kargil conflict.