The Free Lutheran Schools are ministry of the Association of Free Lutheran Congregations (AFLC), which began in 1962. Immediately after the AFLC was formed, there was a desire to start a seminary and Bible school for the purpose of training pastors and equipping of laity.

After prayerful consideration, the AFLC proceeded to establish a theological seminary committed to historic Lutheran theology. The Association Free Lutheran Theological Seminary opened its doors in September, 1964. The founding of the seminary grew out of the need for biblically-trained pastors and Christian workers in the tradition of orthodox Lutheran Pietism. Dr. Iver B. Olson served as the first dean of the seminary, beginning in 1965, followed by Rev. Amos O. Dyrud (1971 to 1981). Dr. Francis W. Monseth became the dean in 1981, and served until his death in 2013. Rev. Robert L. Lee served as interim dean from 2013 until 2015, when Rev. Wade Mobley was called to be the first president of the AFLC Schools and also dean of the seminary. In June 2017, Dr. James Molstre began as dean of the seminary while Mobley continued as president of the schools.

The Association Free Lutheran Bible School began in 1966 with 13 students. Patterned after the former Lutheran Bible Institute in Minneapolis (founded in 1919), the school’s primary goal was to see God transform young people through the teaching of His Word. It was of primary concern among the founders of the AFLC to establish young Christians in the Word of God before college and help believers be equipped for life and ministry in local congregations and communities. Rev. John Strand was the first AFLBS dean, followed by Rev. Richard Snipstead (1968 to 1974), Rev. Ken Moland (1975 to 1984), Rev. Donald Greven (1985 to 1996), Rev. James L. Johnson (1996 to 2006), and Rev. Joel Rolf (2006 to present).

Both schools have experienced growth and development over the decades. Today, the Bible school enrollment ranges from 110 to 130 students per year. Each year, the seminary student body consists of approximately 25 students training for pastoral ministry. The Faculty includes an average of seven full-time instructors who teach in both programs – and several adjunct professors.

In 2014, the Free Lutheran Schools became a member of the Transnational Association of Christian Colleges and Schools (TRACS), having been awarded Candidate Status as a Category III institution by the TRACS Accreditation Commission on October 21, 2014. This status is effective for up to a period of five years. TRACS is recognized by the United States Department of Education, the Council for Higher Education Accreditation and the International Network for Quality Assurance Agencies in Higher Education (INQAAHE).