The Estonian Evangelical Lutheran Church (EELC) was constituted in 1949, when the previous church hierarchy, Eesti Evangeeliumi Luteriusu Kirik, headed by bishop Johan Kõpp, had escaped to Sweden in 1944. When the Soviet Union invaded Estonia in 1940, most Christian organizations were dissolved, church property was confiscated, theologians were exiled to Siberia, and religious education programs were outlawed. World War II later brought devastation to many church buildings. It was not until 1988 that church activities were renewed when a movement for religious tolerance began in the Soviet Union.
Although women had studied theology at Tartu University in the 1920s and some had sought ordination as priests, it was not until 1967 that the first woman, Laine Villenthal, was ordained. In 2014, the church reported that there were 169 men and 43 women serving as ministers.
The Church of Estonia is episcopal in polity, and is led by five bishops, including the archbishop who serves as the Primate. The archbishop has overall control, and under his authority there are four jurisdictions, each with its own Bishop.
During the Soviet occupation of Estonia, the Archbishop went into exile, which resulted in the formation of a parallel church, the Estonian Evangelical Lutheran Church Abroad. Until 2010 this body was independent, with its own Archbishop based in Canada. In 2010 the two churches reunited, and the former overseas church became a diocese of the Estonian Evangelical Lutheran Church, known as the Extra-Estonian Diocese (Estonian: Välis-Eesti piiskopkonna).
As of February 2009, the EELC reported approximately 160,000 baptized members and the EELC Abroad (based in Canada) reported approximately 8,000 baptized members. A previous figure broke down the EELC Abroad into 3,508 members with 12 clergy in the USA and 5,536 members with 11 clergy in Canada. In 2014, the Lutheran World Federation reported the number of registered members as being 180,000. The church reported that it had served 143,895 communicants.
The church is "divided in church circles into conservatives and liberals". In an interview, Archbishop Urmas Viilma stated that the church allows women to be ordained and "will continue to do so", and he stated that, currently, the church only allows celibate gay ministers to be ordained. However, Archbishop Viilma did state that if same-sex marriage is eventually legalized, "then the church will clearly need to redefine itself", but he also stated that "we clearly interpret the Bible to say that practicing homosexuality is sin...but we all are equal in God’s eyes an welcome in church." The Lutherans leaned toward opposing the death penalty, although they took no official stance, and the church does not have a committee "dealing with social-political questions".