The congregation’s organizational meeting was held on November 29, 1954. Its first pastor was the Reverend Dallas Young. Worship services were held in the chapel of Bethany Lutheran Home until the church’s first unit was completed in 1958. St. Mark’s joined the other churches of the Sioux Falls District as a part-owner of Bethany Home.
In 1962, St. Mark’s became part of the newly merged Lutheran Church in America. In 1975, the congregation constructed its distinctive pyramid-shaped sanctuary and expanded its Sunday School, office, and lower-level space. In 1988, St. Mark’s became part of the newly formed Evangelical Lutheran Church in America.