Dr. Lloyd Caswell Kelly, pastor of the Pineville First Baptist Church, founded Clear Creek in 1926. His mission for bringing Christian education to the mountains was twofold. He was inspired to charter Clear Creek Mountain Springs, Inc. “…for educational, recreational and religious purposes, with two objectives in mind: (1) to provide grounds for assemblies and encampments and (2) to establish a base for a ‘mountain mission’ program.” The first sessions for preachers were held from July 18 to August 1, 1926, with twelve students.

In 1946, the General Association of Baptists in Kentucky (now the Kentucky Baptist Convention) approved the school's name, Clear Creek Mountain Preacher’s Bible School. The school's primary focus continued to be educating God-called men and women for Christian ministry.

From 1954 to 1982, Dr. Dennis Merrill Aldridge served as the school's second president. Under his leadership, the school grew to offer a four-year baccalaureate degree. A charter revision in 1957 changed the name to Clear Creek Baptist School.

From 1982 to 1988, Dr. Leon Dennis Simpson served as president. He led the school to receive accreditation from the Accrediting Association of Bible Colleges (now the Association of Biblical Higher Education) in 1986, at which time the name was changed to Clear Creek Baptist Bible College. The Pomeroy Family Life Center was constructed. An innovative class schedule was adopted that encouraged the enrollment of commuting students.

From 1988 to 2007, Dr. Bill D. Whittaker served as president of the college. Early in his administration, the college became debt-free and continues to operate without debt. In 1996, the Association of Biblical Higher Education reaffirmed the college’s accreditation for ten years and then reaffirmed the accreditation until 2017. A successful capital campaign concluded in 1998 with the completion of a new classroom building and nearly a million dollars in additional endowment. In June 1999, the college received accreditation with the Commission on Colleges of the Southern Association of Colleges and Schools, and the accreditation was renewed in June 2005.

From 2007-2022, Dr. Donnie Fox served as the fifth President of Clear Creek since 2007. The President’s home was moved back on campus in the first year of his administration to have better interaction with the campus family. Dr. Fox also operated the college without debt.

Dr. Charlie Goodman was elected as the sixth President of Clear Creek in October 2022 and has filled the role of president since January 1, 2023. Dr. Goodman previously served as the college's Dean of Students, Professor of Theology, and the Director of Graduate Studies. Moreover, he served as a senior pastor for over twenty-three years, pastoring churches in Kentucky, Tennessee, and Virginia. Dr. Goodman holds a B.A., M.A., M.R.E., M.T.S., M.A.R.E., and a D. Min. Dr. Goodman has studied at seven institutions of higher learning.