Ayub Khan was admitted to the Royal Military College, Sandhurst, in 1926. He was commissioned as a second lieutenant on 2 February 1928 in the 19th Punjabis of the 14th Punjab Regiment (better known as 1/14th Punjab Regiment) of the British Indian Army – before this he was attached to the Royal Fusiliers. Amongst those who passed out with him was Joyanto Nath Chaudhuri, who served as Chief of the Army Staff of India from 1962 to 1966 while Ayub was the president of Pakistan. After the standard probationary period of service in the British Army, he was appointed to the British Indian Army on 10 April 1929, joining the 1/14th Punjab Regiment Sherdils, now known as the 5th Punjab Regiment.

He was promoted to lieutenant on 2 May 1930 and to captain on 2 February 1937. During World War II, he was promoted to the temporary rank of lieutenant-colonel in 1942 and was posted in Burma to participate in the first phase of the Burma Campaign in 1942–43. He was promoted to the permanent rank of major on 2 February 1945. Later that year, he was promoted to temporary colonel and assumed the command of his own regiment in which he was commissioned to direct operations in the second phase of the Burma Campaign; however, he was soon temporarily suspended without pay from that command for visible cowardice under fire.

In 1946, he was posted back to British India and was stationed in the North-West Frontier Province. In 1947, he was promoted to brigadier and commanded a brigade in South Waziristan.
When the United Kingdom announced the Partition of British India into India and Pakistan, he was one of the most senior serving officers in the British Indian Army who opted for Pakistan in 1947. At the time of his joining, he was the tenth ranking officer in terms of seniority with service number PA-010.

In the early part of 1948, he was given the command of the 14th Infantry Division in the rank of acting major-general stationed in Dacca, East Pakistan. In 1949, he was decorated with the Hilal-i-Jurat (HJ) by Prime Minister Liaquat Ali Khan for non-combatant service and called back to General Headquarters as the Adjutant General of the army on November of the same year.
As the tenure of General Gracey was nearing its end at the close of 1949, the Pakistan government had called for appointing native commanders-in-chief of the army, air force, and navy and dismissed deputation appointments from the British military. The General Headquarters sent the nomination papers to the Prime Minister's Secretariat for the appointment of commander-in-chief. There were four major generals in the race: Akbar Khan, Iftikhar Khan, Ishfakul Majid, and Nawabzada Agha Mohammad Raza. Among these officers Akbar was the senior, having been com…

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Suhrawardy and Feroz began campaigning to become prime minister and president in the upcoming general elections. Meanwhile, the conservative Pakistan Muslim League, led by its President Abdul Qayyum Khan, was threatening to engage in civil disobedience. These events were against President Mirza hence he was willing to dissolve even Pakistan's One Unit for his advantage.

On 7 October 1958, President Iskandar Ali Mirza abrogated the Constitution of Pakistan of 1956 after sending a letter to Prime Minister Feroz announcing a coup d'état and appointed General Ayub Khan as Chief Martial Law Administrator.

On 13 October, General Ayub Khan assigned Lt. General Wajid Ali Khan Burki the task of improving the efficiency of hospitals and health agencies. Within days, Karachi hospitals showed significant improvement, and the medical services took on a new outlook.

Two weeks later, on 27 October 1958, Ayub Khan carried out his own coup d'état against Mirza. Most of the country's politicians only became aware of the coup the next morning; only U.S. Ambassador to Pakistan James M. Langley was kept fully informed of political developments in the country.

Ayub justified his part by declaring that: "History would never have forgiven us if the present chaotic conditions were allowed to go on any further," and that his goal was to restore a democracy that the "people can understand and work", not to rule indefinitely. When the public was informed, public reactions were mixed. The immediate crackdown on smuggling, corruption, and trafficking won Ayub plenty of support from the commoners. The middle-class and the upper-middle class were more apprehensive.

President Mirza himself was apprehensive, though for a different reason. He had been contemplating replacing Ayub Khan, and it seems that Ayub knew. Immediately after the Supreme Court's Chief Justice Munir justified the coup under the doctrine of necessity, Ayub sent the military into the presidential palace and exiled Mirza to England. This was largely done with the support of: Admiral A. R. Khan, General Azam Khan, Nawab of Kalabagh Amir Khan, General Dr. Wajid Khan, General K. M. Sheikh, and General Sher Bahadur. Air Vice Marshal Asghar Khan was asked by General Ayub Khan to join the Generals to demand Mirza's resignation, but Asghar Khan declined the request, stating that he "found the whole exercise distasteful."

The regime came to power with the intent of instituting widespread reform and 'to bring the country back to sanity'. Li…

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Ayub Khan did not comment on the Bangladesh Liberation War in 1971. He died of a heart attack on 19 April 1974 at his villa near Islamabad at age 66.
Ayub Khan's presidency allied Pakistan with the American-led military alliance against the Soviet Union which helped Pakistan develop its strong economic background and its long-term political and strategic relations with the United States. Major economic aid and trade from the United States and European Communities ultimately led Pakistan's industrial sector to develop rapidly but the consequences of cartelization included increased inequality in the distribution of wealth. After 1965, he became extremely concerned about the arrogance and bossiness of the US over the direction of Pakistan's foreign policy when the US publicly criticized Pakistan for building ties with China and the Soviet Union; he authored a book over this issue known as Friends not Masters.
Ayub Khan began his diary in September 1966, and ended his recordings in October 1972 due to his failing health. The diary covers events such as his resignation from office, the assumption of power by Yahya Khan, the independence of Bangladesh, and the replacement of Yahya by Zulfikar Ali Bhutto. After his death in 1972, the diary was not released to the public for thirty years due to opinions which would have been detrimental to the reputation of powerful individuals at the time. Ayub Khan wanted his diary to be edited by his close associate Altaf Gauhar, but after Ayub Khan's death the six-year-long diary was entrusted to Oxford University Press (OUP) to edit and publish. At OUP, Diaries of Field Marshal Mohammad Ayub Khan, 1966–1972 was edited and annotated by American historian Craig Baxter.
The federal capital was relocated under the Ayub administration from the port city of Karachi to the new and carefully planned city of Islamabad in the mountains in 1965. Facilitated by the World Bank, the Ayub administration became a party to the Indus Waters Treaty with archrival India to resolve disputes regarding the sharing of the waters of the six rivers in the Punjab Doab that flow between the two countries. Khan's administration also built a major network of irrigation canals, high-water dams, and thermal and hydroelectric power stations.
He subsidized fertilizers and modernized agriculture through irrigation development and spurred industrial growth with liberal tax benefits. In the decade of his rule, the GNP rose by 45% and manufactured goods began to overtake such traditional exports as jute and cotton. However, the economists in the Planning Commission alleged that his policies were tailored to reward the elite families and major landowners in the country. In 1968, his administration celebrated the so-called "Decade of Development" when the mass protests erupted all over the country due to an increasingly greater divide between the rich and the poor.
He was one of the signatories of the agreement to convene a convention for drafting a world constitution. As a result, for the first time in human history, a World Constituent Assembly convened to draft and adopt a Constitution for the Federation of Earth.