The first Dutch pastor came to Timor in 1612. There was no continuous ministry until 1821, partly owing to the scarce commercial interest of the Netherlands East Indies Company in the islands. The Netherlands Missionary Society was active in Timor from 1821 to 1863. The church grew slowly and spread to the islands of Roti and Sawu. The Dutch Church in the Indies (Indische Kerk) took over the administration from 1863 to 1942. Only after the 1930s did the GMIT grow and spread to the interior regions of Timor and Alor. Due to mass Christianization the church faced the problem of an insufficient number of leaders to minister to the needs of the people. The church became autonomous in 1947. By that year it had gained a membership of 224,000 in 315 congregations served by 80 ministers. The territory of the GMIT now includes all of the East Nusa Tenggara province, except the Sumba island, and some of GMIT’s congregations are in Sumbawa island, West Nusa Tenggara.

The church still faces the problem that there has been little economic and cultural development in the region. A good deal of education is needed to assist Christians in the transition from a traditional society into the modern period, and to face the effects of rapid social change. The whole church needs to be responsibly involved in community development through schools, health centres, orphanages, literature and vocational training centres. The church attempts to motivate lay people to be active in various church ministries in order that the priesthood of all believers may become real. The primary concerns for 2003-2005 are to promote three models of the church’s ministry: fellowship, diakonia and witness. A significant phenomenon within GMIT are the prayer fellowships of which there are over 2500 throughout the church. They grew out of a spiritual revival that took place in 1966. In recent years they have been influenced by the Pentecostal movement. Since 2001 these groups are officially acknowledged by the GMIT as one of the functional ministry units within the church.  

GMIT aims to build partnership with churches around the world, especially churches in Asia. It maintains special relations with the Protestant Church in the Netherlands, the United Church of Christ (USA), the Uniting Church in Australia, and the Presbyterian Church in Ireland.