John Calvin worked out the presbyterian pattern in practice in Geneva in the 1540s and 1550s, reading the New Testament's references to a plurality of elders governing each congregation as a description of the church's intended government rather than an incidental first-century arrangement. The city's Consistory paired ministers with lay elders in shared oversight of doctrine and discipline, a model that traveled with the students who passed through Calvin's Geneva and carried it home across Reformed Europe.
John Knox studied there and brought the pattern to Scotland, where he and five fellow ministers presented the First Book of Discipline to the Scottish Parliament in 1560, setting out courts of elders as the government of a reformed national church rather than the rule of bishops the old church had known. The system was contested for over a century afterward, alternating with periods of enforced episcopacy under the Stuart kings, until the Church of Scotland's presbyterian government was permanently secured after the Glorious Revolution of 1688 and 1689.
The Westminster Assembly, convened in London through the 1640s with substantial Scottish participation, gave the system its most influential confessional statement, the Westminster Confession of Faith and its companion catechisms, which Presbyterian churches worldwide still hold as their doctrinal standard alongside Scripture.