The GKJ is one of a number of churches on Java which originate from a movement toward Christianity which was initiated by Javanese and European lay people. Afterward the mission bodies came in and organized the Christians into congr under their care. One of these missions was the Nederlandsche Gereformeerde Zendingsvereeniging, which in 1894 was absorbed by the Zending der Gereformeerde Kerken in Nederland. This mission rejected Javanese Christianity as it had developed since the 1870s under the leadership of Sadrach, a Javanese religious leader who had converted to Christianity and spread the Gospel in a truly Javanese way through debates with heads of other religious groups. Most missionaries and the mission agencies in the Netherlands had a negative view of him, mainly because of the honor bestowed on him by his followers, including practices which could be explained as magical. After the rupture with the Sadrach, about 1890, the mission had to make a fresh start. About 1900 it set out to build a new church with a more traditional Western outlook. The negative attitude of the mission toward expressions of traditional Javanese culture, such as thewayang(puppet play), has to be seen as the reverse side of the introduction of Western (Dutch-language) education and modern health care on a scale not equalled in any mission field in Indonesia. The mission also stressed its activity in (Christian) organizations in the social and political field, although it frowned on Indonesian nationalism. In accordance with its Calvinist principles it systematically built up the church organization, starting from the local congregation (1900) to the Synod level. In 1931, when there were 7,500 Christians in 31 congr, the first Synod was held, under Javanese leadership; in 1932 the church accepted a church order. However, as in other mission fields, the missionaries held an important position as advisors until 1942.
After World War II the missionaries were received back, with the condition that they should not interfere in the internal affairs of the church. The GKJ was more ready than its mother church to join ecumenical organizations (1948 WCC, which was joined by GKN only in 1969; 1950 PGI). Many or its members joined the struggle for Indonesian independence, and many played an important role in the Christian political party PARKINDO and other mass organizations. The church experienced sustained growth, with a peak occurring after the suppression of leftist parties in 1965-1967.The union of the four Javanese-speaking churches in Central and East Java, which at one time had been set as a distant goal by the missions, was never realized. In 1949 the GKJ united with the congregationalist-type congr in the northern half of Central Java; in 1953 a number of those congr split off again and formed what was to become the GKJTU. In 1997 the GKJ accepted a new confession of faith,Poko-poko ajaran Gereja Kristen Jawa, written in the form of a catechism. Through several foundations, in which GKJ and GKI-Jawa Tengah work together, the church is active in the field of education (Lembaga Perencanaan dan Pembinaan Pendidikan Kristen) and health care (YAKKUM, which runs the great Bethesda hospital in Yogyakarta). The Lembaga Pembinaan dan Pengaderan runs a lay training center. The church publishes a magazine. The GKJ considers February 17, 1931, as its birth date.