Lutheran immigrants, from various parts of Sweden and some from Norway, had settled near Annandale in the year 1886 or before. Pastors Gustaf Petetson of Stockholm and J.A. Levine of Cokato had made home missionary journeys preaching the word of God to them. It was in order to provide for spiritual needs for these pioneer men and women that the ministry of St John's Lutheran Church was established. There are descendants of the charter members, who are members of the present church.

The name of the original church was The Swedish Evangelical Lutheran St. John's Church of South Side. In 1887 a building committee of five persons was given the task of preparing plans for the building of a church. This building was on the northeast corner of Harrison and 3rd. On May 10, 1959 ground was broken to build a new church building at the present site; In 1972 a new educational wing was added to complete the building.

The Church Register of the original church records 38 communicants and 30 children (68 baptized members). The services were held in the Swedish language (except for funerals) until 1918. In the early 20th century the growth of the congregation remained fairly constant as the 1914 annual report showed that. The congregation had grown to 170 baptized members and the 1945 annual report shows 191 baptized members. In the 1997 pictorial directory, baptized members were 950. At the end of the year 2000 St. John's had a baptized membership of 1,225. On December 16, 2001, the current sanctuary building was dedicated. In 2006, St. John's had a baptized membership of 1,449.