The Malagasy Lutheran Church was founded by Norwegian missionaries who first came in 1866 and began work in the central part of the island. The work was supported by Norwegian Lutherans in the U.S. The first missionary sent by immigrant Lutherans from the U.S. was Pastor John P. Hogstad from Augsburg Seminary. He and his wife Lena arrived in 1888 in Fort Dauphin. Pastor Hogstad was an outstanding pioneer who opened Lutheran work throughout the southern area of Madagascar. The Hogstads were joined in 1889 by a second couple, Rev. Erik and Mrs. Caroline Tou, and many more missionaries were sent in the following years.

Early missionaries suffered many hardships. Many of them died from malaria, sometimes after only a year or two in Madagascar. During parts of the early 20th century, the French colonial government was very uncooperative with mission efforts and even closed down churches. But the church took hold, especially among tribal peoples who had no previous contact with Christianity.

The Norwegian and American missions cooperated in numerous projects. The seminary at Ivory, Fianarantsoa, was established by Norwegian missionaries and became the seminary for a united Lutheran church. This seminary, which still uses its century-old main building, now trains pastors at the graduate level. Several Malagasy faculty received advanced theological training through scholarship programs of the ELCA. In addition to thi "flagship" seminary, there is a network of regional seminaries which train pastors at a lower academic level.

The Malagasy Lutheran Church was established as an independent church in 1950, with 1800 congregations and 180,000 members. It was the first former "mission field"church to be accepted into the Lutheran World Federation. It has enjoyed tremendous growth in numbers, and currently has over 1.5 million members in 13 synods, cared for by 1,000 pastors and 15,000 catechists, making it one of the largest Lutheran churches in the world. The Malagasy Lutheran Church places a high priority on evangelism and leadership development, but faces a big challenge in keeping up with needs and demands.

The church has a unique approach to spiritual and physical care of people who suffer from physical illness, mental illness, or demonic oppression. Through an indigenous revival movement, selected church members receive training as "shepherds," giving them skills for special ministries with the sick. Some villages are set aside to provide compassionate Christian care as well as instruction in the Christian faith.

The Malagasy Lutheran Church maintains a huge health care program, including nine hospitals and thirteen dispensaries. Community based primary health care is foundational, and special projects include a school of nursing, child survival, family planning, and AIDS prevention. There are also extensive church-related programs in agriculture and development.