First military era (1958-1971)

The Dominion was dissolved on 23 March, 1956 and replaced by the Islamic Republic of Pakistan with the last Governor-General, Iskandar Mirza, as the first president. Just two years later the military took control of the nation.Field Marshal Ayub Khan became president and began a new system of government called Basic Democracy with a new constitution,by which an electoral college of 80,000 would select the President. Ayub Khan almost lost the controversial 1965 presidential elections to Fatima Jinnah.During Ayub's rule, relations with the United States and the West grew stronger. Pakistan joined two formal military alliances — the Baghdad Pact (later known as CENTO) which included Iran, Iraq, and Turkey to defend the Middle East and Persian Gulf against the Soviet Union;and SEATO which covered South-East Asia.However, the United States adopted a policy of denying military aid to both India and Pakistan during the Indo-Pakistani War of 1965 over Kashmir and the Rann of Kutch.

Between 1947 and 1971, Pakistan consisted of two geographically separate regions, West Pakistan and East Pakistan. During the 1960s, there was a rise in Bengali nationalism in East Pakistan, and of allegations that economic development and hiring for government jobs favoured West Pakistan. An independence movement in East Pakistan began to gather ground. After a nationwide uprising in 1969, General Ayub Khan stepped down from office, handing power to General Yahya Khan, who promised to hold general elections at the end of 1970. On the eve of the elections, a cyclone struck East Pakistan killing approximately 500,000 people. Despite the tragedy and the additional difficulty experienced by affected citizens in reaching the voting sites, the elections were held and the results showed a clear division between East and West Pakistan. The Awami League, led by Sheikh Mujibur Rahman, won a majority with 167 of the 169 East Pakistani seats, but with no seats in West Pakistan, where the Pakistan Peoples Party led by Zulfikar Ali Bhutto, won 85 seats. However, Yahya Khan and Bhutto refused to hand over power to Mujib.

Meanwhile, Mujib initiated a civil disobedience movement, which was strongly supported by the general population of East Pakistan, including most government workers. A round-table conference between Yahya, Bhutto, and Mujib was convened in Dhaka, which, however, ended without a solution. Soon thereafter, the West Pakistani Army commenced Operation Searchlight, an organized crackdown on the East Pakistani army, police, politicians, civilians, and students in Dhaka. Mujib and many other Awami League leaders were arrested, while others fled to neighbouring India. On 27 March 27 1971, Major Ziaur Rahman, a Bengali war-veteran of the East Bengal Regiment of the Pakistan Army, declared the independence of East Pakistan as the new nation of Bangladesh on behalf of Mujib. The crackdown widened and escalated into a guerrilla warfare between the Pakistani Army and the Mukti Bahini (Bengali "freedom fighters").Although the killing of Bengalis was unsupported by the people of West Pakistan, it continued for 9 months. India supplied the Bengali rebels with arms and training, and, in addition, hosted more than 10 million Bengali refugees who had fled the turmoil.

In March, 1971, India's Prime Minister, Indira Gandhi expressed sympathy for the East Pakistani independence movement, opening India's borders to refugees and providing other assistance. Following a period of covert and overt intervention by Indian forces, open hostilities broke out between the two countries on December 3, 1971. In East Pakistan, the Pakistani Army led by General A. A. K. Niazi, had already been weakened and exhausted by the Mukti Bahini's guerrilla warfare. Outflanked and overwhelmed, the Pakistani army in the eastern theatre surrendered on December 16, 1971, with nearly 90,000 soldiers taken as prisoners of war. The figures of the Bengali civilian death toll from the war vary greatly, depending on the sources. Although Pakistan's official report, by its Hamood-ur-Rahman Commission, places the figure at only 26,000, other sources put the number between 1.25 to 1.5 million. Highest figure, reported only in the media, is 3 million.

The result was the emergence of the new nation of Bangladesh.Discredited by the defeat, General Yahya Khan resigned. Bhutto was inaugurated as president and chief martial law administrator on 20 December, 1971.