Northwestern Theological Seminary, a part of Northwestern Schools, was founded in Minneapolis in 1935 by Dr. William Bell Riley, a noted fundamentalist leader. In the decade after Dr. Riley's passing, financial pressures forced Northwestern's Board of Trustees to close the seminary. Students, seminary faculty, and other supporters urged Dr. Richard V. Clearwaters, pastor of the Fourth Baptist Church of Minneapolis, to fill this vacuum in ministry through the establishment of a fundamental Baptist seminary.

With the knowledge and encouragement of the administration of Northwestern Schools, this was done. The Fourth Baptist Church agreed to provide accommodations for the fledgling school within its own facilities. Thus Central Baptist Theological Seminary of Minneapolis was born, opening on September 11, 1956, with a student body of thirty-one students from ten states and a faculty of seven.

Within its first decade, Central Seminary grew to a student body of over 100 students. As Fourth Baptist Church prospered, the seminary enjoyed expanded facilities. In 1965, Central Seminary established a radio station and began a radio ministry.

Dr. Douglas R. McLachlan succeeded Dr. Clearwaters as pastor of Fourth Baptist Church in 1982 and succeeded him as president of Central Baptist Theological Seminary during the 1986-1987 school year. Dr. Ernest D. Pickering served as the seminary's third president from 1988 to 1993. In the providence of God, Dr.McLachlan answered the call to return to the pastorate of the Fourth Baptist Church and presidency of Central Baptist Seminary in 1994. Dr. McLachlan resigned his ministries as chairman of the departments of Bible, Pastoral Theology, and Graduate Studies at Northland Baptist Bible College and returned to Minneapolis. Under Dr. McLachlan's leadership, Fourth Baptist Church and Central Baptist Theological Seminary relocated to an excellent facility in the Minneapolis suburb of Plymouth in 1998. In 2003, Dr. Kevin T. Bauder was elected to be Central Seminary's fourth president. During his tenure, Dr. Bauder oversaw the expansion of the library and the continued development of the Romanian campus. In 2011, Dr. Sam Horn became the new president of the seminary.

Central Seminary graduates serve in ministry in nearly every state of the United States, as well as in mission works on many foreign fields.