He was assassinated by the revenge seeking counter-coupists led by Theophilus Danjuma on 29 July 1966 at Ibadan, along with General Johnson Aguiyi-Ironsi, the Head of State and Supreme Commander of the Armed Forces of the Federal Republic of Nigeria; who had arrived in Ibadan on 28 July 1966 to address a conference of natural rulers of Western Nigeria. By dusk, he was through with the assignment and was prepared to head back to Lagos, but his host, Lt. Colonel Fajuyi, convinced him to spend the night at the Government House, Ibadan.
The bloody overthrow of the civilian regime of Prime Minister Tafawa Balewa’s government had taken place six months earlier in which the prime minister and other top government functionaries especially of Northern Nigerian extraction were killed.
The coup (seen then as a revolution) was successful in the North but failed in the South. Ironically, Aguiyi-Ironsi who did not participate in the violent bloodletting inherited the pieces of a shattered republic by virtue of his seniority in the armed forces. Yet, he was a victim of the counter-coup that claimed his life alongside his courageous host, Fajuyi. Fajuyi did all he could to persuade Danjuma not to kill Ironsi but when he saw that Danjuma insisted, he told him that he could not allow him unless he (Fajuyi) was killed first. This Danjuma did before going after Ironsi himself.