During the reign of James VI of Scotland, a large number of Scottish Presbyterians emigrated to Ireland, chiefly to Ulster.

However, after the Restoration, nonconforming ministers were removed from parishes of the Established Church, but no matter the opinions of the king on religion, the Irish administration could not afford to alienate such a substantial Protestant population and Presbyterianism was allowed to continue in the country, with the stipends of ministers paid through the regium donum – literally 'the King's gift'.

From the 1690s, Presbyterian congregations, now organised in the Synod of Ulster, enjoyed practical freedom of religion, confirmed by the Toleration Act 1719.

However, their members remained very conscious both of continuing legal disabilities under the penal laws and of economic hardship as many were tenant farmers and objected to the payment of tithes to support the Church of Ireland.

[8][clarification needed] In the nineteenth century, a belief that some of those who did not subscribe to the Westminster Confession were in fact Arian provoked a new phase of the conflict.

This led to the restoration of obligatory subscription to the Westminster Confession within the Synod of Ulster and facilitated union with the Seceders in 1840 to create the General Assembly of the Presbyterian Church in Ireland, whose first moderator was Samuel Hanna.

[12] The PCI is involved in education, evangelism, social service and mission in a number of areas around the world:[13] Apart from the seats for worshippers, the inside of a Presbyterian church building (often called the meeting house) is dominated by four items of furniture.

[17] In 2021 the General Assembly agreed to ‘…direct the Trustees to employ a 'divest and engage' strategy in relation to companies producing or using fossil fuels, thereby divesting from those that derive more that 10% of their turnover from oil and gas extraction (the coal, oil and gas majors), and engaging with companies that derive more than 10% of their turnover from the use of fossil fuels encouraging them to make clear commitments to the targets for global heating and carbon emission reduction as set out in the COP 21 Paris Agreement; reporting back to the 2022 General Assembly.

'[18] On the issue of dealing with the legacy of the Troubles, the Church's Council for Public Affairs has commented on "the right of victims and survivors to seek due process and justice in the courts.

The Council’s report expressed its 'deep disquiet at the current proposals' stating that, 'whilst the Stormont House Agreement (SHA) was not perfect, it did set out a broader, four-strand framework to address legacy issues.

We are on public record stating our support for all four key principles outlined in the SHA, especially the right of victims and survivors to seek due process and justice in the courts.

"[19] The Church is active in social work and provides services to those with addictions and offending behaviours, and who require supported housing through specialist facilities.

[22] However, in June 2006, the General Assembly (GA) voted to ban its ministers from blessing same-sex relationships, clarifying the previous ambiguity.

In June 2018, the General Assembly held a debate "the specific theological question of what constitutes a credible profession of faith and how it is to be understood and applied in [the] particular pastoral circumstances" of same-sex couples.

"[25]The Assembly subsequently agreed with this report, and voted 'That appropriate training be offered to Kirk Sessions on the theology and practice of the Church's understanding of 'a credible profession of faith' and the pastoral guidelines on homosexuality.'