Started as a Sunday School mission of the First Baptist Church of Minneapolis, it met in members' homes until it grew large enough for its own building. Jewett Chapel, on the corner of 11th Avenue North and Lyndale Ave, housed the church until it was large enough to build a new sanctuary at 18th Avenue North and Dupont Avenue in 1885.

In 1920, the church voted to buy land and build on the corner of Fremont Avenue North and 21st Avenue. A long period of growth and expansion followed; by 1954 the church averaged over 700 for Sunday services. In 1974, Fourth Baptist Church constructed a 2,000 seat auditorium adjacent to the original auditorium on Fremont Avenue North. It remained there until 1998 when the congregation voted to sell the old properties and build new facilities in Plymouth, a suburb of Minneapolis. A new ministry, Family Baptist Church, was planted in the original north Minneapolis neighborhood, and many of Fourth Baptist's members remained to strengthen this new inner-city ministry.

God has specially blessed Fourth Baptist Church by providing three great Bible teachers to lead this ministry through the last 60 years. From 1940 to 1982, Dr. Richard V. Clearwaters pastored the church, providing a solid foundation in Biblical teaching, while overseeing th establishment of Fourth Baptist Christian School, Central Baptist Theological Seminary, and WCTS radio. Dr. Ernest Pickering provided a strong pulpit ministry from 1988 to 1993. From 1982 to 1987, Dr. Douglas R. McLachlan pastored Fourth Baptist Church. He returned as pastor in 1994, and continues the tradition of applying God's timeless truth to our needs today.