He attended Saint Mary"s Catholic School in Kabba from 1949 until 1956, Mount Saint Michael"s Secondary School in Aliade, Benue State from 1957 until 1962, and Ss. He completed his religious studies in Rome in 1969, and was ordained as a priest on 3 August of that year. He finished his Licentiate of Sacred Scripture in 1973 and earned his doctorate in 1976.
He was previously President of the Christian Association of Nigeria, President of the Catholic Bishops" Conference of Nigeria and Bishop of Ilorin. Peter & Paul Major Seminary in Bodija, Ibadan from 1963 until 1965. Ahmadu Bello, Premier of Nigeria"s Northern Region, had offered him a scholarship to study abroad.
Onaiyekan taught at Saint Kizito"s College, Isanlu in 1969.
He became rector of Saint Clement Junior Seminary in Lokoja in 1971. He became Vice Rector of Ss.
Peter & Paul in 1977. In October 1980, Pope John Paul II gave Onaiyekan a five-year appointment to the International Theological Commission.
In November, he joined the International Catholic/ Methodist Dialogue Commission.
Onaiyekan was consecrated as Bishop of Ilorin, Kwara State on 6 January 1983. In 1990 he became Coadjutor Bishop of the Diocese of Abuja, and when the diocese became a Metropolitan See in 1994, John Onaiyekan became the Metropolitan of Abuja. Onaiyekan was elected to the position of Vice-President of the Catholic Bishops" Conference of Nigeria (CBCN) in 1994, and President of that organization in 2000.
Archbishop Onaiyekan was named Pax Christi International"s 2012 Peace Laureate.
On Tuesday, 18 September 2012, Archbishop Onaiyekan was appointed by Pope Benedict XVI to serve as one of the papally-appointed Synod Fathers for the upcoming October 2012 Ordinary General Assembly of the Synod of Bishops on the New Evangelization. He was created a Cardinal by Pope Benedict XVI in a consistory on 24 November 2012.
As Cardinal-Priest he was assigned the titular church of San Saturnino. He will hold these memberships until his 80th birthday.
He was one of the cardinal electors who participated in the 2013 papal conclave that elected Pope Francis.
Cardinal Onaiyekan was appointed by Pope Francis as the Apostolic Administrator ad nutum Sanctae Sedis of the diocese of Ahiara in Imo State, eastern Nigeria on Wednesday, 3 July 2013. His Vice President was Daniel Okoh, President of the Organisation of African Instituted Churches. However, he was not re-elected.
In 2010 he was succeeded by Ayo Oritsejafor.
On Thursday, 31 January 2013, Pope Benedict XVI appointed Cardinal Onaiyekan to serve as a Member of the Congregation for the Doctrine of the Faith (CDF) and as a Member of the Presidential Committee of the Pontifical Council for the Family.