A Scottish man named John Knox (1514-1571) began embracing Protestant ideas in Scotland while the Reformation was gaining influence in Germany and Switzerland, but he was captured by the French in 1547, and was forced to become a galley slave for nineteen months. After his release, Knox made his way to England and stayed there a few years, then when Mary Tudor, a Roman Catholic, ascended to the English throne, he went into exile on the European continent. It was during this time in his life that he made his way to Geneva and Zurich, the two centers of Reformed theology and influence. Some years later, the Protestant lords of Scotland asked Knox to return to Scotland and help with the reformation of the Church there. Knox and other Protestants worked to reform the Church of Scotland according to many of the principles of Reformed theology.

Knox also helped to write a book of discipline which detailed a kind of church government in which ministers, elders, and deacons, among others, shared in the decision-making process of the church. In the decades after Knox's death, this system of government would be developed further into what would be called the Presbyterian form of government, which added to Knox's system the use of presbyteries, synods, and even a General Assembly to help govern the Church of Scotland.

However, there was intense debate for almost a century after Knox's death between church leaders of the Presbyterian persuasion and church leaders in favor of an Episcopal form of government. By the late 17th century, the Presbyterian form of government had triumphed and had become the official church government of the Church of Scotland. These are the origins of the Presbyterian Church as we know it. Though theologically all Presbyterian churches are part of the Reformed theological family, in terms of church government, only some Reformed churches utilize the Presbyterian form of government. Hence, the term "Presbyterian" refers to a type of church government within the Reformed tradition and not to a separate branch of theology.