In 1884, the first Protestant Church was built by Suh Sang-Ryun in Sorai, Hwanghae Province in what is now North Korea. Suh was a lay person who was baptized in Manchuria and returned to Korea to evangelize. One of the particular characteristics of Korean Christianity is that Koreans themselves, on their own initiative, began to translate the Gospel and build churches before foreign missionaries came to Korea. One of the most important accomplishments of the early Protestant Christians was the printing of the New Testament in Hangul, the Korean alphabet which all could read. Insightful and radical, the decision to print the Gospel in Hangul was highly significant because the elite and the government used the Chinese alphabet. Rev. John Ross, a Scottish Presbyterian minister serving in Manchuria, worked with several Koreans on the translation. In addition, schools, hospitals, orphanages and churches were built by early Christians.

In 1907, the Presbyterian Church in Korea was established. In 1912, the first General Assembly was held. Presbyterian missionaries from Australia, the United States, and Canada came to Korea in increasing numbers in the following years.

During the Japanese occupation, the church faced many extreme difficulties. As Japan increased its pressure on Koreans by banning the use of the Korean language and Korean names, it also attempted to force Christians to worship at the Shinto shrine.

In 1953 the Presbyterian Church faced another serious challenge. This challenge centered around theology and methods of biblical study taught at the then Chosun Theological Seminary, now the Graduate School of Theology, Hanshin University. From the early days of the Presbyterian Church, many Koreans were completely influenced by the conservative, fundamentalist theology propounded by the missionaries. There were some, however, who strove to be independent of this influence. Eventually a conflict erupted between these two groups. Those who learned liberal theology and methods of historical critical interpretation of the Bible came into conflict with ruling and authoritarian members of the Presbyterian Church who held a fundamentalist faith and view of the Bible ingrained in them by the missionaries. A series of incidents led up to the decisive crisis of 1953, including Rev. Kim Young-Ju's rejection of Moses' authorship of the Pentateuch, in 1934; Rev. Kim Choon-Bae's liberal and feminist interpretation of Paul's teachings regarding women; a controversy over the Abingdon Bible Commentary in 1935 which was directly related to the historical critical method; and a debate about the literal inspiration and infallibility of the Bible in 1952.

The authoritarian leaders of the Presbyterian Church accused the faculty of Chosun Theological Seminary of teaching heresy and of denying the infallibility of the Bible. The seminary, under the leadership of Rev. Dr. Kim Jae-Joon, was committed to freedom of learning and conscience as well as the theological tradition of Calvin and the Reformed church. In addition to the teaching of historical critical interpretation of the Bible, the faculty of Chosun Theological Seminary were deeply committed to developing superior theological education and articulating Christian theology from a Korean perspective. The conservative and fundamentalist faction would not accept this theology and the difference between the two groups became irreconcilable.

This conflict divided the Presbyterians in 1953 into The Presbyterian Church in the Republic of Korea [PROK] and The Presbyterian Church of Korea [PCK]. The missionary community was also divided over this matter. The US-American and Australian Presbyterian missionaries supported the PCK, while the Canadian missionaries supported the PROK.