On 15 January 1966, Major Emmanuel Ifeajuna and other junior Army officers (mostly majors and captains) attempted a coup d'état. The two major political leaders of the north, the prime Minister, Sir Abubakar Tafawa Balewa and the Premier of the northern region, Sir Ahmadu Bello were executed by Major Nzeogwu. Also murdered was Sir Ahmadu Bello's wife and officers of Northern extraction. Meanwhile, the President, Sir Nnamdi Azikiwe, an Igbo, was on an extended vacation in the West Indies. He did not return until days after the coup. There was widespread suspicion that the Igbo coup plotters had tipped him and other Igbo leaders off regarding the impending coup. In addition to the killings of the Northern political leaders, the Premier of the Western region , Ladoke Akintola and Yoruba senior military officers were also killed. The coup, also referred to as "The Coup of the Five Majors", has been described in some quarters as Nigeria's only revolutionary coup.[42] This was the first coup in the short life of Nigeria's nascent second democracy. Claims of electoral fraud were one of the reasons given by the coup plotters.

This coup was however seen not as a revolutionary coup by other sections of Nigerians , especially in the Northern and Western sections and latter revisioninsts of Nigerian coups, mostly from Eastern part of Nigeria have belatedly maintained to widespread disbelief amongst Western and Southern Nigerians that the majors sought to spring Action Group leader Obafemi Awolowo out of jail and make him head of the new government. From there, they would dismantle the Northern-dominated power structure. However, their efforts to take power were thwarted by Johnson Aguiyi-Ironsi, an Igbo and loyalist head of the Nigerian Army, who suppressed coup operations in the South. The majors surrendered, and Aguiyi-Ironsi was declared head of state on 16 January.[43][44]

Aguyi-Ironsi suspended the constitution and dissolved parliament. He then abolished the regional confederated form of government and pursued unitary like policies heithero favoured by the NCNC, having apparently been influenced by some NCNC political philosophy. He however appointed Colonel Hassan Katsina, son of Katsina emir Usman Nagogo, to govern the Northern Region, indicating some willingness to maintain cooperation with this bloc.[45] He also preferentially released northern politicians from jail (enabling them to plan his forthcoming overthrow).[46] Aguyi-Ironsi rejected a British offer of military support but promised to protect British interests; however … Britain participated in overthrow?

Ironsi fatally did not bring the failed plotters to trial as required by then-military law and as advised by most northern and western officers,rather, coup plotters were maintained in the military on full pay and some were even promoted while apparently awaiting trial. The coup, despite its failure and since no repercussion was meted out to coup plotters and since no significant Igbo political leaders were affected was widely perceived as having benefited mostly the Igbo. Most of the known coup plotters were Igbo and the military and political leadership of Westerrn and Northern regions had been largely bloodily eliminated while Eastern military/political leadership was largely untouched. However Ironsi, himself an Igbo, was thought to have made numerous attempts to please Northerners. The other event that also fuelled the so-called "Igbo conspiracy" was the killing of Northern leaders, and the killing of the Colonel Shodeinde's pregnant wife by the coup executioners. Despite the overwhelming contradictions of the coup being executed by mostly Northern soldiers (such as John Atom Kpera, later military governor of Benue State), the killing of Igbo soldier Lieutenant-Colonel Arthur Unegbe by coup executioners, and Ironsi's termination of an Igbo-led coup, the ease by which Ironsi stopped the coup led to suspicion that the Igbo coup plotters planned all along to pave the way for Ironsi to take the reins of power in Nigeria.

Colonel Odumegwu Ojukwu became military governor of the Eastern Region at this time.[48] On 24 May 1966, the military government issued Unification Decree #34, which would have replaced the federation with a more centralized system. The Northern bloc found this decree intolerable.[49]

In the face of provocation from the Eastern media which repeatedly showed humiliating posters and cartoons of the slain northern politicians, on the night of 29 July 1966, northern soldiers at Abeokuta barracks mutinied, thus precipitating a counter-coup, which have already been in the planning stages. The counter-coup led to the installation of Lieutenant-Colonel Yakubu Gowon as Supreme Commander of the Nigerian Armed Forces. Gowon was chosen as a compromise candidate. He was a Northerner, a Christian, from a minority tribe, and had a good reputation within the army.

It seems that Gowon immediately faced not only a potential standoff with the East, but secession threats from the Northern and even the Western region.[50] The counter-coup plotters had considered using the opportunity to withdraw from the federation themselves. Ambassadors from Britain and the United States, however, urged Gowon to maintain control over the whole country. Gowon followed this plan, repealing the Unification Decree, announcing a return to the federal system