Subsequent to the Partition of India in 1947 and the First Kashmir War, the name "Gilgit Agency" was adopted by Pakistan to refer to the territory which formed a de facto dependency of Pakistan from 1947 to 1970, but the name ceased to be used when the territory was merged into the Northern Areas. This Pakistani "Gilgit Agency" was administered directly from Islamabad, separately from the neighbouring state of Azad Kashmir and the princely states of Hunza and Nagar. It did not include the district of Kargil and the subdivision of Ladakh which had been a part of the British Gilgit Agency. The Pakistani Agency bordered the Sinkiang region of China to the northeast, the Indian state of Jammu and Kashmir to the south, Baltistan to east, and the North-West Frontier Province to the west.
The local rulers of these territories continued to appear at the Kashmir Durbars until 1947. The events of Partition and the subsequent invasion of Kashmir by Pakistani tribals led to most of the former Gilgit Wazarat becoming part of Pakistan-administered Kashmir, but most of the Ladakh Wazarat, including the Kargil area became part of Indian-administered Kashmir. The Line of Control represents the de facto border of India and Pakistan
Initially, the Gilgit Wazarat was not absorbed into any of the provinces of West Pakistan, but were ruled directly by political agents of the federal government of Pakistan. In 1963, Pakistan entered into a treaty with China to transfer part of the Gilgit Wazarat to China, (the Trans-Karakoram Tract), with the proviso that the settlement was subject to the final solution of the Kashmir dispute.
The dissolution of the province of West Pakistan in 1970 was accompanied by change of the name of the Gilgit Agency to the Northern Areas. In 1974, the states of Hunza and Nagar and independent valleys of Darel-Tangir, which had been de facto dependencies of Pakistan, were also incorporate into the Northern Areas.
Pakistan and India continue to dispute the sovereignty of the territories that had comprised the Gilgit Agency.