Yakubu Gowon joined the Nigerian army in 1954, receiving a commission as a Second Lieutenant on 19 October 1955, his 21st birthday. He also attended both the Royal Military Academy Sandhurst, UK (1955 – 56), Staff College, Camberley, UK (1962), as well as the Joint Staff College, Latimer, 1965. He saw action in the Congo (Zaire) as part of the United Nations Peacekeeping Force, both in 1960 - 61 and in 1963. He advanced to battalion commander rank by 1966, at which time he was still a Lieutenant Colonel.

Up until that year Gowon remained strictly a career soldier with no involvement whatsoever in politics, until the tumultuous events of the year suddenly thrust him into a leadership role, when his unusual background as a Northerner who was neither of Hausa or Fulani ancestry nor of the Islamic faith made him a particularly safe choice to lead a nation whose population were seething with ethnic tension.

In January 1966, he became Nigeria's youngest military chief of staff at the age of 32, because a military coup d'état by a group of mostly Igbo junior officers under Major Chukwuma Kaduna Nzeogwu led to the overthrow of Nigeria's civilian government. In the course of this coup, mostly northern and western leaders were killed, including Sir Abubakar Tafawa Balewa, Nigeria's Prime Minister; Sir Ahmadu Bello, Sardauna of Sokoto and Premier of the Northern Region; and Samuel Akintola, Premier of the Western Region, as well as several high ranking Northern army officers. The then Lieutenant Colonel Gowon returned back from his course at the Joint Staff College, Latimer, UK, two days before the coup - a late arrival that possibly exempted him from the coupist hit list. In contrast, only a single Igbo officer lost his life. This gave the coup an ethnocentric cast that aroused the suspicions of Northerners, and the subsequent failure by Major General Johnson Aguiyi-Ironsi (who was the head of state following the January 1966 coup - with Gowon his Chief of Staff) to meet Northern demands for the prosecution of the coup plotters further inflamed Northern anger. It should be noted that there was significant support for the coup plotters from both the Eastern Region as well as the mostly left-wing "Lagos - Ibadan" press.

Then came Ironsi's Decree Number 34, which proposed the abolition of the federal system of government in favor of a unitary state, a position which had long been championed by the Southern parties - the NCNC and the AG. This was perhaps wrongly interpreted by Northerners as a Southern (Eastern, Midwestern and Western Regions) attempt at a takeover of all levers of power in the country. The North lagged badly behind the Western and Eastern regions in terms of education due to their religious related unacceptance of western education early, while the mostly Igbo Easterners were already present in the federal civil service. On 29 July 1966, while Ironsi was staying at Government House in Ibadan, northern troops led by Major Theophilus Danjuma and Captain Martin Adamu stormed the building, seized Ironsi and his host, Lieutenant Colonel Adekunle Fajuyi, and subsequently had the two men stripped naked, flogged and beaten, and finally shot. Other northern troops, led by Lieutenant Colonel Murtala Mohammed, the real leader of the counter coup and who later succeeded Yakubu Gowon as head of state, then seized the Ikeja airport in Lagos. Several Igbo and Eastern minority officers were killed during the counter coup.

The original intention of Murtala Mohammed and his fellow coup plotters seems to have been to engineer the secession of the Northern region from Nigeria as a whole, but they were subsequently dissuaded of their plans by several advisors, amongst which included a number of high ranking civil servants and judges, and importantly emissaries of the British and American governments who had interests in the Nigerian polity. The young officers then decided to name Lieutenant Colonel Gowon, who apparently had not been actively involved in events until that point, as Nigerian Head of State. On ascent to power Gowon reversed Ironsi's abrogation of the federal principle.

In the meantime, the July counter coup had unleashed pogroms against the Igbo throughout the Northern Region. Hundreds of Igbo officers were murdered during the revolt, and in the North, as commanding officers either lost their control of their troops or actively egged them on to violence against Igbo civilians, it did not take long for Northerners from all walks of life to participate. Tens of thousands of Igbos were killed throughout the North. The persecution precipitated the flight of more than a million Igbo towards their ancestral homelands in eastern Nigeria. Lieutenant Colonel Chukwuemeka Odumegwu Ojukwu, the military governor of the Eastern region who did not allow attempts by Northern soldiers stationed in his region to replicate the massacres of Igbo officers, argued that if Igbo lives could not be preserved by the Nigerian state, then the Igbo reserved the right to establish a state of their own in which their rights would indeed be respected.

There arose tension between the Eastern region and the northern controlled federal government lead by Gowon. On 4–5 January 1967, in line with Ojukwu's demand to meet for talks only on neutral soil, a summit attended by Gowon, Ojukwu and other members of the Supreme Military Council was held at Aburi in Ghana, the stated purpose of which was to resolve all outstanding conflicts and establish Nigeria as a confederation of regions. The outcome of this summit was the Aburi Accord.

The Aburi Accord did not see the light of the day, as the Gowon led government had huge consideration for the possible revenues, especially oil revenues which were expected to increase given that reserves having been discovered in the area in the mid 1960s. It has been said without confirmation that both Gowon and Ojukwu had knowledge of the huge oil reserves in the Niger Delta area, which today has grown to be the mainstay of the Nigerian economy.

In a move to check the influence of Ojukwu's government in the East, Gowon announced on 5 May 1967 the division of the 3 Nigerian regions into 12 states - North-Western State, North-Eastern state, Kano State, North-Central State, Benue-Plateau State, Western State, Lagos State, Mid-Western State, and, from Ojukwu's Eastern Region, a Rivers State, a South-Eastern State, and an East-Central State. The non-Igbo South-Eastern and Rivers states which had the oil reserves and access to the sea, were carved out to isolate the Igbo areas as East-Central state.

One controversial aspect of this move was Gowon's annexing of Port Harcourt, a large city in the Niger Delta, in the South of Nigeria comprising of the Ikwerres, sitting on some of Nigeria's largest reserves, into the new Rivers State, emasculating the migrant Igbo population of traders there. The flight of many of them back to their villages in the 'Igbo heartland' in Eastern Nigeria where they felt safer was alleged to be a contradiction for Gowon's "no victor, no vanquished" policy, when at the end of the war, the properties they left behind were reclaimed by the rivers state indigenes.

Minority ethnicities of the Eastern Region were rather not sanguine about the prospect of secession, as it would mean living in what they felt would be an Igbo dominated nation. Some non-Igbos living in the Eastern Region either refrained from offering active support to the Biafran struggle, or actively aided the federal side by enlisting in the Nigerian army and feeding it intelligence about Biafran military activities. However, some did play active roles in the Biafran government, with N.U. Akpan serving as Secretary to the Government, Lt. Col (later Major-General) Philip Effiong, serving as Biafra's Chief of Defence Staff and others like Chiefs Bassey and Graham - Douglas serving in other significant roles.

On 30 May 1967, Ojukwu responded to Gowon's announcement by declaring the formal secession of the Eastern Region, which was now to be known as the Republic of Biafra. This was to trigger a war that would last some 30 months, and see the deaths of more than 100,000 soldiers and over a million civilians, most of the latter of which would perish of starvation under a Nigeria imposed blockade. The war saw a massive expansion of the Nigerian army in size and a steep increase in its doctrinal and technical sophistication, while the Nigerian Air Force was essentially born in the course of the conflict. However, significant controversy has surrounded the air operations of the Nigerian Forces, as several residents of Biafra, including Red Cross workers, foreign missionaries and journalists, accused the Nigerian Air Force of specifically targeting civilian populations, relief centers and marketplaces. Gowon has steadfastly denied those claims, along with claims that his army committed atrocities such as rape, wholesale executions of civilian populations and extensive looting in occupied areas; however, one of his wartime commanders, Benjamin Adekunle seems to give some credence to these claims in his book, while excusing them as unfortunate by-products of war.

The end of the war came about on 13 January 1970, with Colonel Olusegun Obasanjo's acceptance of the surrender of Biafran forces. The next day Obasanjo announced the situation on the former rebel radio station Radio Biafra Enugu. Gowon subsequently declared his famous "no victor, no vanquished" speech, and followed it up with an amnesty for the majority of those who had participated in the Biafran uprising, as well as a program of "Reconciliation, Reconstruction, and Rehabilitation", to repair the extensive damage done to the economy and infrastructure of the Eastern Region during the years of war. Unfortunately, some of these efforts never left the drawing board. In addition to this, Gen. Gowon's administration's policy of giving 20 pounds to everyone who had a bank account in Nigeria before the war, regardless of how much money had been in their account, was criticised by foreign and local aid workers, as this led to an unprecedented scale of begging, looting and robbery in the former Biafran areas after the war.

The postwar years saw Nigeria enjoying a meteoric, oil-fueled, economic upturn in the course of which the scope of activity of the Nigerian federal government grew to an unprecedented degree, with increased earnings from oil revenues. Unfortunately, however, this period also saw a rapid increase in corruption, mostly bribery, of and by federal government officials; and although the head of State himself, Gen. Gowon, was never found complicit in the corrupt practices, he was often accused of turning a blind eye to the activities of his staff and cronies.

Another fateful decision made by Gowon at the height of the oil boom was to have severely negative repercussions for the Nigerian economy in later years, although its immediate effects were scarcely noticeable - his indigenization decree of 1972, which declared many sectors of the Nigerian economy off-limits to all foreign investment, while ruling out more than minority participation by foreigners in several other areas. This decree provided windfall gains to several well connected Nigerians, not the least important of whom was MKO Abiola (who Fela Anikulapo Kuti was later to lampoon as "International Thief-Thief" for his role as an inactive, nominal majority shareholder in a joint venture with ITT), but proved highly detrimental to non-oil investment in the Nigerian economy.

Apart from winning the civil war and keeping the country together, general Gowon's time also saw development of the Country's capital - Lagos - into an international city, the creation of Twelve states, the introduction of odd and even days to manage Lagos traffic and the expansion of government bureaucracy.

Gowon subsequently went into exile in the United Kingdom, where he acquired a Ph.D. in political science as a student at the University of Warwick. He lived in north London / Hertfordshire border, and very much became part of the English community in his area, where he served a term as Church warden in the local church.

In February 1976, Gowon was implicated in the Coup d'état led by Lt. Col Buka Suka Dimka, which resulted in the death of the now Gen Murtala Mohammed. According to Dimka's "confession", he met with Gowon in London, and obtained support from him for the coup. In addition, Dimka mentioned before his execution that the purpose of the Coup d'état was to re-install Gowon as Head of State. As a result of the coup tribunal findings, Gowon was declared wanted by the Nigerian government, stripped of his rank in absentia and had his pension cut off. Gen Gowon was finally pardoned (along with the ex-Biafran President, Emeka Ojukwu) during the Second Republic under President Shehu Shagari.

He returned to Nigeria in the 1980s, and in the 1990s he formed a non-denominational religious group, Nigeria Prays. Still based in the UK, General Gowon today serves an 'elder statesman' role in African politics, operating (for example) as an official observer at the Ghanaian presidential elections 2008. Furthermore, Gen. Gowon is also involved in the Guinea Worm Eradication Programme as well as the HIV Programme with Global Fund of Geneva. Gowon founded his own organization in 1992 called the Yakubu Gowon Centre. The organization is said to work on issues in Nigeria such as good governance as well as infectious disease control including HIV/AIDS, guinea worm, and malaria.