Christianity was brought into Namibia under the auspices of the London Missionary society (LMS) in 1806. During the first part of the 19th century, Lutherans Missionaries from Germany and Finland began their mission activities in Namibia.

The Finnish Missionary Society (FMS / FELM) started mission work in northern Namibia in July 1870. As the result of their efforts, congregations and parishes were established, bringing about institutionalization of the Evangelical Lutheran Ovambo- Kavango Church (ELOC) with Birger Eriksson as its first president.

The church developed out of the work of the Finnish Missionary Society that began in 1870 among the Ovambo and Kavango people in the northern area of what became German South West Africa. In 1954, an independent church known as the Evangelical Lutheran Ovambo-Kavango Church (ELOC) was established with Birger Eriksson as its first president.

The first Namibian bishop of ELOC, Leonard Auala, played a notable role in the struggle for Namibia’s independence. In 1971 an open letter was written jointly with Moderator Paulus Gowaseb of the Rhenish Mission‘s United Evangelical Lutheran Church in South West Africa (later known as the Evangelical Lutheran Church in the Republic of Namibia) to the Prime Minister of South AfricaB.J. Vorster, which declared their church’s opposition to the continued rule of South Africa and the acceptance of the recommendation by the International Court of Justice for the withdrawal of South Africa’s mandate and a transition period towards independence In 1984, ELOC’s name was officially changed to its current iteration, the Evangelical Lutheran Church in Namibia (ELCIN) to reflect its national presence on the Namibian scene. In 1992, the church was demarcated into two dioceses; the Eastern and Western Diocese each led by a Bishop. One of the bishops is elected as the Presiding Bishop of whole ELCIN.

Auala’s successor, Kleopas Dumeni, also played an important role in highlighting the plight of Namibians under South African rule.

In 2007, ELCIN together with the Evangelical Lutheran Church in the Republic of Namibia and the German-speaking Evangelical Lutheran Church in Namibia (GELK) formed the United Church Council: Namibia Evangelical Lutheran Churches, with the ultimate aim of becoming one united national Lutheran church.

The church was originally led by a Moderator, elected from amongst the clergy. In the 1960s the church adopted episcopal polity and was subsequently led by a bishop. In 1992, the church was divided into two dioceses, the Eastern Diocese and the Western Diocese, each led by its own bishop, and since 1996 a Presiding Bishop has been elected to preside over the whole ELCIN.