Pakistan is administratively divided into four provinces, one federal territory, and two disputed territories: the provinces of Punjab, Sindh, Khyber Pakhtunkhwa, and Balochistan; the Islamabad Capital Territory; and the administrative territories of Azad Jammu and Kashmir and Gilgit–Baltistan. As part of the Kashmir conflict with neighbouring India, Pakistan has also claimed sovereignty over the Indian-controlled territories of Jammu and Kashmir and Ladakh since the First Kashmir War of 1947–1948. It also has a territorial dispute with India over Junagadh, but has never exercised administrative authority over either regions. All of Pakistan's provinces and territories are subdivided into divisions, which are further subdivided into districts, and then tehsils, which are again further subdivided into union councils.

Pakistan inherited the territory comprising its current provinces from India following the Partition of India on 14 August 1947. Two days after independence, the Muslim-majority Murshidabad district in Bengal was moved out of the Dominion of Pakistan and put within the Dominion of India due to a boundary adjustment by the Radcliffe Commission which was aimed at keeping the Hooghly River entirely within India. At its inception, Pakistan consisted of two wings, which were separated from each other by around 1,600 kilometres (990 mi) of Indian territory. The western wing consisted of a merger of the North-West Frontier Province, West Punjab, Sind Province, and Baluchistan CCP. The eastern wing consisted of East Bengal. What later became the Princely states of Pakistan chose at first to remain independent.

In 1948, Karachi was separated from Sind Province to form the Federal Capital Territory. In 1950, the North-West Frontier Province absorbed the princely states of Amb and Phulra while West Punjab (designated 'West' to distinguish it from India's Punjab in the east) was renamed to simply Punjab. In 1952, the four princely states in the southwest formed the Baluchistan States Union.

In 1955, the One Unit policy was launched by then-Prime Minister Muhammad Ali Bogra, whereby all the provinces and princely states of the western wing were merged to form the provincial wing of West Pakistan, with Lahore serving as its provincial capital. Simultaneously, East Bengal was redesignated as East Pakistan, with Dacca serving as its provincial capital. The One Unit policy aimed to reduce expenditure and to eliminate provincial prejudices, but the military coup of 1958 brought difficulties when the first military President, Ayub Khan, abolished the office of the Chief Minister of West Pakistan in favour of Governor rule.

On 7 September 1958, after four years of negotiations (including six months of intense negotiations), Pakistan purchased the enclave of Gwadar from Oman for ₨.5.5 billion (US$3 million; approximately $22,410,311.42 in 2017). Gwadar formally became a part of Pakistan on 8 December 1958, ending 174 years of Omani rule. In 1960, the federal capital was moved from Karachi to Rawalpindi and in 1961, the Federal Capital Territory was also merged into West Pakistan. In 1966, the capital was again moved to the newly constructed city of Islamabad. In 1962, Dacca was made the legislative capital of the country due to East Pakistan's high population. Following the 1963 Sino–Pakistan Agreement, a part of the Gilgit Agency (controlled by Pakistan since the First Kashmir War) was formally relinquished by Pakistan to the People's Republic of China (the Trans-Karakoram Tract/Shaksgam Valley in northeastern Kashmir) with the provision that the settlement was subject to the final solution of the Kashmir dispute between India and Pakistan.

In 1970, the second military President, Yahya Khan, abolished the political structure of West Pakistan and established four new provinces: Sindh, Punjab, Balochistan and the North-West Frontier Province. In 1971, the Bengali-majority wing of East Pakistan seceded from the Pakistani union following the Bangladesh Liberation War, consequently forming the independent People's Republic of Bangladesh. In 1974, the remaining princely states of Hunza and Nagar were abolished and their territories merged into the Gilgit Agency, following which the Northern Areas were formed. In 1975, portions of the districts of Peshawar and Dera Ismail Khan were separated to form the Federally Administered Tribal Areas. In 1981, the region surrounding Islamabad was separated from Punjab province, and renamed to the Islamabad Capital Territory.

In August 2000, divisions were abolished as part of a plan to restructure local governments, followed by elections in 2001. Many of the functions previously handled at a provincial level had been transferred to individual districts and tehsils. In 2008, the government restored the former divisions and appointed commissioners.

In 2009, the Northern Areas were renamed to Gilgit-Baltistan, and retained its formal status as an autonomous territory. In 2010, the North-West Frontier Province was formally renamed to Khyber Pakhtunkhwa. In 2018, the National Assembly of Pakistan and Khyber Pakhtunkhwa Provincial Assembly passed the historic FATA Merger Bill with the Twenty-Fifth Constitutional Amendment. On 31 May 2018, the final step in the merger of the Federally Administered Tribal Areas with Khyber Pakhtunkhwa was completed, as then-President Mamnoon Hussain signed the 25th Constitutional Amendment Bill into law. The amendment's signing abolished the Federally Administered Tribal Areas as a separate political entity and merged them into the province of Khyber Pakhtunkhwa.