The early beginning of the College of Theology can be traced to the Bible School whose establishment was conceived together with that of the Jaro Industrial School, the precursor of Central Philippine University. The idea to establish two schools was conceived when, on December 2, 1904, the Philippine Baptist Mission Conference, the organization of the early American Baptist Missionaries, voted "to establish two schools: an industrial school for boys and a Bible School to train pastors and other Christian workers." The Rev. William O. Valentine was appointed administrator of the two schools.

In June 1905, the Bible School was opened in the hoome of the Valentines. There were 12 pupils with some "Bible Women" who attended as auditors. On October 1, 1905, the Jaro Industrial School was opened on a 24-hectare land in Jaro. The leadership of the Bible School was turned over to the Rev. Henry Munger who conducted classes off campus. In 1907, Dr. Eric Lund became principal and classes were held at the Mission Press building where Lund was doing his Scripture translation work. When Dr. Lund leftin 1912, the Bible School was closed. It was reopened in 1913 by Rev. Alton Bigelow. It was under his leadership that the school began to have to have a definite direction in its development.

In 1923, the Jaro Inductrial School became Central Philippine College. In April of the following year, the Bible school became an organic part of the College. A program leading to the degree of Bachelor of Theology was offered. Those who enrolled were men students who were trained to be pastors of the churches. In 1936, through the guidance of Rev. Bigelow, the school became the Department of Theology of Central Philippine College.

While the Bible School was established for the training of men to be pastors, the training of women to be missionaries began in 1907 with the establishment of the Baptist Missionary Training School (BMST) under the leadership of Miss Anna B. Johnson and Celia Sainz. Both were sent to the Philippines by the Women's American Baptist Foreign Mission Society. Miss Johnson was assigned in Capiz. The BMTS continued to develop separately from the Bible School until 1938, when it was merged with the Department of Theology of Central Philippine College. With the merging of the two schools two degree programs were offered-the Bachelor of Theology and the Bachelor of Science in Religious Education.

On April 1, 1953, Central Philippine College was granted government recognition as a university. Following this, the Department of Theology became the College of Theology. Gradually, the leadership of the university and the College of Theology turned over to the Filipinos. A significant part of this Filipinization process look place in 1966 when Dr. Rex D. Drilon became the first Filipino President of the University.

The College of Theology is an integral part of Central Philippine University. Its purpose is to train pastors and Christian leaders for the Christian churches, particularly the churches of the Convention of Philippine Baptist Churches. It cooperated with evangelical and ecunumical organizations here and abroad. It is a member institution of the Association of Theological Education in South East Asia and the South East Asia Graduate School of Theology. It is fraternally related through the Convention of Philippine Baptist Churches to the Board of International Ministries of the American Baptist Churches, the Autralian Baptist Mission Society, the Baptist World Alliance, the Asian Baptist Fellowship, the National Council of Churches in the Philippines and other Christian organizations.