The East Java Christian Church has been a missionary church from the beginning. It grew from a spontaneous movement among the Javanese in the middle of the 19th century. In the 1830s groups of Javanese believers near Surabaya were brought into contact with the gospel by the activities of European lay people; the first baptism occurred in 1843. In the 1850s the Dutch mission (NZG) took over and started what it considered to be a necessarily long process of bringing the church to maturity. This process was concluded by the convening of the first synod in 1931, when the church had 23,000 baptized members, in 45 local parishes. But, as elsewhere in Indonesia, the NZG remained as a “guide towards adulthood” until 1942. So great was its influence that the GKJW considers itself a daughter church of the Netherlands Reformed Church (now Protestant Church in the Netherlands). The coming of the Japanese brought the end of missionary domination. During and after World War II the church went through hard times. After 1950 a slow but steady growth began, which peaked after the elimination of communism in 1965-1967. From the beginning, the GKJW has been a rural church; many congregations were founded by clearing forests and establishing Christian villages on the reclaimed land. The other churches in East Java are based in the cities. Together they constitute 1.5 million (including Roman Catholic) of the 34 million population of East Java, the overwhelming majority (95.5 percent) being Muslim. In 1995 and 1996 riots occurred several times, resulting in severe damage to Christian lives and property.

The GKJW has a number of hospitals, clinics, a small number of schools for elementary to senior high level and an orphanage. In 1987 the church commenced its first six-year comprehensive church development plan, which consists of programmes for the development of theological activities, community life, Christian service, Christian witness, and stewardship. Pastors are trained at the theological school in Malang. The GKJW is connected with the Duta Wacana Christian University in Yogyakarta.

The church considers December 11, 1931 as its birth date. It uses three languages: Indonesian, Javanese and Madurese. Its organization is presbyterian-syn-odal. Since 1981 the GKJW has been in relationship with the United Evangelical Mission in Germany. It has partnership relations with the Protestant Church in the Netherlands, the Evangelical Church in Rhineland (Germany) and the Presbyterian Church (USA).

The theme of the church for 1999-2004 was: Realizing the year of the Lord’s favour to all people (Isaiah 61:1-3). The theme for 2005-2010 is: Realizing the family of God as the Lord’s favour to all people (Psalm 128).