The history of the Presbyterian Church of New Zealand began with the arrival at Port Nicholson, Wellington, on 20 February 1840, of the Rev. John Macfarlane of the Established Church of Scotland. Macfarlane officiated at the opening of the first Scots Church (now St. Andrew's) in New Zealand on Sunday, 7 January 1844. When the effects of the disruption of the Scottish Church (1843) began to be felt in the Antipodes, a petition was drawn up in 1851 by a group of Scots in Wellington and forwarded to the Free Church of Scotland asking that an ordained minister of that church be secured. The prayer of the petition was granted and in 1853 the Rev. John Moir arrived in Wellington to be the minister of the second Presbyterian Church (now St. John's).
In the South Island the history of the Presbyterian Church began with the Scottish Free Church Lay Association which played an important part in the founding of the Otago settlement. The religious interest of the forties, stimulated by the disruption crisis, gave its inspiration to the colonising project, the lay body working closely in conjunction with the Church to bring it to fruition. Together they transplanted to the new land a branch of the Free Church of Scotland along with its rich social and cultural soil. In November 1847 two ships – the Philip Laing and the John Wickliffe – set sail for New Zealand with the first group of Free Church settlers. The “Moses” of the settlers was Captain William Cargill and the “Aaron” the Rev. Thomas Burns, a nephew of Robert Burns, the Scottish poet. With them there also came a schoolmaster, James Blackie. The manner in which the Free Church settlers, right from the inception of the Otago settlement, made provision for church and school indicated how deeply imbued they were with the ideals of religion and education.
In Auckland the first Presbyterian service was held in 1842, but it was the Scottish disruption that stimulated the Presbyterians settled there to form a congregation and to request Dr Thomas Chalmers, the leader of the Free Church, to select for them a minister. The outcome was the sending out of the Rev. G. A. Panton and the opening of St. Andrew's Church in 1849. Panton's ministry was very brief and he was succeeded by the Rev. David Bruce who became a leader in church extension work throughout the North Island.
In 1851 a group of Gaelic-speaking Highlanders under the leadership of a 74-year-old patriarch, the Rev. Norman McLeod, came to New Zealand in ships built with their own hands after a sojourn in Nova Scotia, and settled at Waipu in Northland. The descendants of these settlers have played an important part in the upbuilding of the Presbyterian Church in the northern part of New Zealand.
Organised Presbyterian work in Hawke's Bay began in 1859 with the founding of St. Paul's Church, Napier, under the ministry of the Rev. Peter Barclay, and in 1860 in Taranaki with the settlement in New Plymouth of the Rev. John Thom.
Among the first settlers in Canterbury were five Scottish families, but it was not until 1854 that the Presbyterians there requested the Colonial Committee of the Free Church of Scotland to secure a minister for them. In response to this request the Rev. Charles Fraser came in 1857 as the first minister of St. Andrew's Church, Christchurch.
The Presbyterian settlers of Nelson were at first ministered to by the Rev. John Macfarlane, but in 1849 the Rev. T. D. Nicholson came to be the first minister of Trinity Church, Nelson. In 1857 Nicholson moved into Marlborough and was instrumental in erecting a church at Renwicktown, the first church of any denomination in the district.
The founding of the Presbyterian Church on the romantic West Coast was assisted by the visits of the Rev. Charles Fraser, of Christchurch, who prepared the way for the settlement at Hokitika in 1867 of the Rev. John Gow.
South of the Waitaki, with the steady extension of settlement, it was realised that the Rev. Thomas Burns could not carry the burden of ministering to the Otago settlers alone. In 1854 the Rev. William Will and the Rev. William Bannerman arrived in Otago to assist him and so made possible the constitution of the presbytery of Otago, the first presbytery in New Zealand.
Southland was part of the parish of the Rev. William Bannerman until 1860, when the Rev. A. H. Stobo was settled in Invercargill as the first minister of First Church.