The beginnings of the JELC go back to 1892 when the first missionaries to Japan were sent by the United Synod of the South, a predecessor of the Lutheran Church in America, arrived in Yokohama.

The first worship service in Japan was observed on Easter Sunday of 1893 in the city of Saga on the island of Kyūshū under the leadership of James Augustin Brown Scherer and R. B. Peery assisted by a Japanese co-worker, Ryohei Yamanouchi [ja].

The first expatriate workers were soon joined by missionaries from the American Danish Lutheran Church (1898) and Finland (1900).

Shortly before the outbreak of the Second World War, the United Church of Christ in Japan (日本キリスト教団, Nihon Kirisuto Kyoudan) (UCCJ) was formed under state pressure and all Protestant denominations were forced to merge with this new body.

Despite having a comparatively small membership with most congregations having less than 50 members, the JELC has sent successive missionaries to serve among Japanese immigrants in Brazil, serving with the Evangelical Church of the Lutheran Confession in Brazil, as well as to the United States among expatriate Japanese.

This includes an emphasis on youth evangelism as well as fostering the Christian growth of youth, the strengthening of the laity and lay led evangelism, clergy continuing education and a program for clergy review, as well as church/congregational restructuring in order to strengthen outreach.

The Kamagasaki Diaconia Center in the slums of Osaka includes child care, mutual learning, problem study, and community projects.