In 1965, he played a vital role in executing Operation Grand Slam in Indian-administered Kashmir during the Second India–Pakistan War and was assigned to assume the army command in October 1966 by President Ayub Khan.

Holding the country's first general election in 1970, he barred power transition to the victorious Sheikh Mujibur Rahman from East Pakistan, leading to mass protests in the provincial wing and a call for sovereignty.

On 25 March 1971, Khan ordered Operation Searchlight in an effort to suppress Bengali nationalism, which led to the Bangladesh Liberation War.

The wars resulted in the surrender of Pakistani forces and East Pakistan succeeded as Bangladesh, after which Yahya Khan resigned from the army command and transferred the presidency to Zulfikar Ali Bhutto.

Khan is viewed negatively in both Bangladesh, where he is seen as the architect of the genocide, and Pakistan, where his failure to prevent the country's disintegration is considered a national tragedy.

In this year, he was instrumental in not letting the Indian officers shift books from the famous library of the Staff College, Quetta where Yahya was posted as an instructor at the time of the partition.

He played a pivotal role in sustaining the support for President Ayub Khan's campaign in the 1965 presidential elections against Fatima Jinnah.

The uprising spread to East Pakistan and gathered strength, adding to a tense political climate that had worsened following President Ayub Khan's implementation of the 1966 Tashkent Agreement and sacking of Foreign Minister Zulfikar Ali Bhutto.

[21] Ayub Khan tried to quell the revolt by making concessions to opposition groups including the Pakistan Peoples Party (PPP) and the Awami League (AL), but demonstrations continued.

"[10][27] Yahya Khan's new military government featured several active duty military officials: When Yahya Khan assumed the office on 25 March, he inherited a two-decade constitutional problem of inter-provincial ethnic rivalry between West Pakistan, which was almost exclusively Muslim and was dominated by the Punjabi-Pashtun-Mohajir peoples, and East Pakistan, whose population was largely ethnically Bengali and approximately three-fourths Muslim (as of the 1961 Census).

[16] The American political scientist Lawrence Ziring observed: Yahya Khan has been widely portrayed as a ruthless uncompromising insensitive and grossly inept leader....

While Yahya cannot escape responsibility for these tragic events, it is also on the record that he did not act alone.... All the major actors of the period were creatures of a historic legacy and a psycho-political milieu which did not lend itself to accommodation and compromise, to bargaining and a reasoned settlement.

Ahmad, then Deputy Chairman of the Planning Commission of Pakistan told Henry Kissinger that the state "had now realized that it would have to sacrifice some of its economic growth rate for the sake of social reform and of meeting the problem of disparity in the allocation of resources" between the two wings, and noted that the loss of direct US military aid meant "Pakistan had had to cut back resources devoted to the development budget in order to finance the procurement of military equipment.

[16] Yahya also made an attempt to accommodate the East Pakistanis by abolishing the principle of parity, in the hope that a greater share in the assembly would redress their wounded ethnic regional pride and ensure the integrity of Pakistan.

The Pakistan Muslim League (PML), led by Nurul Amin, was the only party to have representation from all over the country, but it failed to gain the mandate to run the government.

[43][44] A government-in-exile formed across the border in India and proclaimed the independent state of Bangladesh, appointing Sheikh Mujibur Rahman as its head despite him being in a West Pakistan prison at the time.

The original plan for Operation Searchlight envisioned taking control of the major cities on 26 March 1971 and then eliminating all opposition, political or military[45] within one month.

[47] Bangladeshi authorities claim that 3 million people were killed,[48] while the Hamoodur Rahman Commission, an official Pakistani Government investigation, put the figure as low as 26,000 civilian casualties.

However, the captured territory was given back to Pakistan in the Simla Agreement signed on 2 July 1972 between Indira Gandhi and Zulfikar Ali Bhutto.

"[53] Personal initiatives of President Yahya had helped to establish the communication channel between the United States and China, which would be used to set up the Nixon's trip in 1972.

[59] Witness accounts presented by Kissinger pointed out that Nixon made specific proposals to Prime Minister Gandhi on a solution for the crisis, some of which she heard for the first time, including a mutual withdrawal of troops from the Indo-East Pakistan borders.

[62] The United States was secretly encouraging the shipment of military equipment from Iran, Turkey, and Jordan to Pakistan, offering to replenish those countries' weapons stocks later[63] despite Congressional objections.

To forestall further unrest, on 20 December 1971, he handed over the presidency and government to Zulfikar Ali Bhutto, the ambitious leader of the (at that time) powerful and popular People's Party.

Within hours of Yahya Khan stepping down, President Bhutto reversed the Judge Advocate General Branch's verdict against Sheikh Mujibur Rahman and instead released him, allowing him to fly to London.

[66][67] Indian journalist Dewan Berindranath argued that Yahya turned to alcohol and womanizing when he gained power, as a coping mechanism to deal with stress, and that when he was a soldier he was known for being morally upright, abstaining from partying unlike other officers and instead preferring to spend time with his family and also practicing Islamic rituals such as the fast of Ramadan, eventually quoting Ayub Khan who said that "Give me half a dozen officers of the calibre and moral standards of Yahya Khan and I can show you what can Pakistan do as a great nation of the Islamic world.

[69] More generally, Yahya used the intelligence services (the ISI and the IB) "to keep secular political parties under check", mobilizing the Information Ministry for propaganda and pushing the idea that they put "Islam and Pakistan in danger.

The rest-house was secured by military personnel, and his communications with the outside world were heavily restricted to prevent any interference with the confidential commission's investigation.

Additionally, a stroke which left him half paralysed[10] and his obesity had worsened his health, making him increasingly frail and incapable of resuming a normal life.

[citation needed] Yahya remained under house arrest until 1977, when he was released from custody by martial law administrator General Fazle Haq due to his failing health.

[89] Yahya Khan was awarded HPk, HJ, SPk, NePl but then stripped of his service honours by the Zulfikar Ali Bhutto regime.