The Synod of Otago & Southland has its origins in the beginnings of the Otago Province, in 1848. Many of the Scottish Presbyterian emigrants who came to Otago at this time in search of a better life were members of the 'Free Kirk,' formed after the Disruption of 1843 split the Church of Scotland. Although there was already a Presbyterian Church in New Zealand, the independent southern settlers established their own Presbyterian Church. The Waitaki River was the boundary between the two.
As settlement expanded, the southern Presbyterians built a network of congregations throughout Otago and Southland. They set up a management structure of church courts, and in 1866 established the Synod as the ruling body for the church. The Synod administered church business, held together the southern presbyteries, and distributed the growing income from church property trusts.
When the southern and northern Presbyterian Churches were united in 1901, it was on condition that the substantial trusts which were the special endowment of the southern church remained in the south. The Synod of Otago and Southland became a court of the united church, but retained control of these trusts. The Synod remains the sole regional court of the national church.