On the evening of September 27th, 1887, Saemoonan Church was founded as the first organized church in Korea under the guidance of Reverend H.G. Underwood. On that evening, Rev. Underwood and 14 baptized Korean Christians participated in a worship service held at a home in Chungdong, Seoul where one member was baptized and two members appointed as elders of the church. In the early years of Saemoonan Church, a Korean-style house in front of Underwood's private residence was used as the church building.As church members increased dramatically, a new church building was constructed at the site now known as City Bank building (across from Gyeonghui Palace) In May 1910, the church moved to the current location.

Saemoonan Church established branch churches in Seoul and the surrounding Kyeonggi area, thus fulfilling its role as the mother church. Internally, the church also continued to strengthen. In 1904, Song Sunmyeong, a Saemoonan member, was selected as an elder and actively worked to vitalize the church. After 1910, Reverend Seo Kyeongjo, one of Korea’s first seven reverends, served as an Associate Reverend and actively strengthened the church’s internal organization. In 1920, Reverend Cha Jaemyeong, a former deacon and elder of the church, was appointed as the second reverend of the church and first Head Pastor – the first of its kind in Korea. Reverend Cha re-organized the monthly committee meeting and choir, and thereby worked to strengthen Saemoonan’s functional capacity. . Reverend Kim Yeongju, the third reverend to be appointed in 1944, devoted himself to the reconstruction and revival of the church after Korea’s liberation from Japan in 1945. Tragically, he was abducted to North Korea during the Korean War.

In December 1955, with Reverend Kang Sinmyeong’s appointment asfourth reverend, the church experienced a revival of the Holy Spirit and continued to increase in reputation. The church worked to re-organize its administration and various organizations The H.G. Underwood Memorial Hall was constructed in September 1967 and the church pushed ahead with many activities including volunteer services for rural communities, medical missions and started evening educational programs in the city. As the total number of church members significantly increased after Reverend Kang's appointment, the current church building was built on November 1972 and “85 years of Saemoonan Church” was published on April 1973.

On April 1981, Reverend Kim Dongik was appointed as the fifth reverend and “100 years of Saemoonan Church” was published in 1994. During his tenure, various overseas mission activities were undertaken, including the establishment of Vladivostok Seminary in 1996, and the consecration of the Korean-Thai Mission Center in 1998. Appointed as the sixth reverend on September 2000, Reverend Lee Sooyoung erfocused on expanding the educational infrastructure, including Saemoonan Teachers’ Institute, Saemoonan Volunteer Training Center (2007), and Saemoonan Academy (2009). As the mother church of Korea's Presbyterianism and the first messenger of the gospel to Korea, Saemoonan Church has demonstrated a deep-rooted faith to mission work, cultivated a spirit of interdominational cooperation among churches, and affirmed our commitment to press forward in our mission.