The seminary was established by Christians in the Evangelical Presbyterian Church, (which later merged with the Reformed Presbyterian Church, General Synod to form Reformed Presbyterian Church-Evangelical Synod), who believed that their denomination, born out of resistance to rising liberal influences, needed a strong theological school of its own. In 1956, Covenant College and Seminary began with eleven students on a plot of land a few miles west of St. Louis, Missouri (having split from Faith Theological Seminary). The seminary continued to grow in both size and reputation in the years that followed. In 1964, having outgrown its space, the liberal arts undergraduate school, Covenant College, along with its students, faculty, and staff, moved to Lookout Mountain, Georgia to the site of a former luxury hotel. In 1966, the two institutions formally divided. In 1982, following another denominational merger (known as the "joining and receiving") between the Reformed Presbyterian Church and the Presbyterian Church in America, Covenant Seminary became the national seminary of the PCA, which elects and oversees the work of the seminary's Board of Trustees.
As of 28 April 2012, Mark Dalbey was the Acting President of Covenant Theological Seminary. On this date his office announced the decision by the Board of Trustees, that Bryan Chapell, the current President of Covenant Seminary, would be transitioning from sabbatical to a newly created position of Chancellor on 1 June 2012. On that date Dalbey would assume the position of Interim President. 1 February 2013 brought the announcement that Chappell had taken a pastoral call in Illinois with resignation as Chancellor effective 15 April 2013. On September 26, 2013, Dalbey was inaugurated as President.
^Greg Edwards (7 May 2007). "Praying in style". St. Louis Business Journal. American City Business Journals. Retrieved 2012-05-19. Covenant Seminary, the seminary of the Presbyterian Church in America, has broken ground on a...three-story...administrative...building on Conway Road...scheduled for completion in August 2008, said Dr. Bryan Chapell, seminary president.
^Rick Nutt, "The Tie That No Longer Binds: The Origins of the Presbyterian Church in America." In The Confessional Mosaic: Presbyterians and Twentieth-Century Theology, Milton J. Coalter, John M. Mulder, and Louis B. Weeks (eds.), Westminster John Knox Press, 1990, 066425151X, pp. 236–256.