It is the second-largest province in the Anglican Communion, as measured by baptised membership (not by attendance), after the Church of England.

In 1989 the Diocese of Abuja was created on the area of the new capital of Nigeria with Peter Akinola as first bishop.

In December 1996 five more mission dioceses were added in the north — Kebbi, Dutse, Damaturu, Jalingo and Otukpo — and their respective first bishops elected.

The vision elaborated was: The Church of Nigeria (Anglican Communion) shall be; Bible-based, spiritually dynamic, united, disciplined, self supporting, committed to pragmatic evangelism, social welfare and a Church that epitomizes the genuine love of Christ.

[14]The program of action included among others additional translations of the liturgy, establishing a lay fundraising team, establishing a legal support to ensure freedom of religion and worship, establishing theological colleges and universities, internet access for all dioceses, training evangelists, priests and their wives, social welfare programs, hospitals, secondary schools, literacy courses and setting up cottage industries.

[17] The rapid expansion has continued, and as of 2012 there were 14 archbishops, heading 14 ecclesiastical provinces, with a total of 161 dioceses.

After the ordination of a partnered gay man, Gene Robinson, as a bishop of the Diocese of New Hampshire, in the United States, he threatened that it was a measure that could split the Anglican Communion.

Also in 2005, Archbishop Akinola criticised the Church of England for allowing clergy in same-sex civil partnerships saying that "[it] proposes same-sex marriage ‘in everything but name’ and that the proposal to extract a promise from gay clergy who register for civil unions to abstain from sexual relations is ‘totally unworkable’ and 'invites deception and ridicule'.

[24] Now reconstituted as the Church of Nigeria North American Mission, CONNAM consists of two U.S. dioceses primarily composed of Nigerian immigrants.

[29] The Church of Nigeria was represented at GAFCON III, held in Jerusalem, on 17–22 June 2018, by a 472 members delegation, the largest from any Anglican province.

[34] In October 2009, the Nigerian church's leadership reacted to the Vatican's proposed creation of personal ordinariates for disaffected traditionalist Anglicans by saying that although it welcomed ecumenical dialogue and shared moral theology with the Roman Catholic Church, the current GAFCON structures already meet the spiritual and pastoral needs of conservative Anglicans in Africa.