The church came into being in 1949 as a result of the union of the Christian Javanese Church in South-Central Java and the Christian Javanese Church of North-Central Java. The former was founded in 1931 through the missionary work of the Reformed Churches in the Netherlands (now the Protestant Church in the Netherlands), the latter was founded in 1937 through the work of the Salatiga Mission, sponsored by the “Waisen- und Missionsanstalt” of Germany. The GKJ acknowledges the Apostles’ Creed and the Heidelberg catechism. In government it is presbyterian.

The Javanese Christian Churches carry on missionary work among Javanese transmigrants in Sumatra and in central Java through a number of agencies. These include schools for education at all stages, teacher training schools and hostels for students; general hospitals and maternity hospitals; a bookshop; orphanages and an old people’s home; and Sunday schools. Apart from full-time missionaries, the church has a number of its members working in a voluntary, part-time capacity. There are many Bible study groups.