In August 1951, the Philippine Baptist Mission of the Foreign Mission Board of the Southern Baptist Convention, U.S.A., authorized the establishment of a theological school and requested Dr. Frank P. Lide to lead in the project. The Philippine Baptist Theological Seminary and Bible School, Inc. was established in 1952. The first session began on July 15, 1952 at the Chinese Baptist Church of Baguio with seven Chinese students enrolled. A building was rented very near the church to house the students. At that time there were five faculty members. The English language division opened the following year. The present permanent campus was occupied in 1955.

Dr. Frank P. Lide served as President from the beginning of the school until 1964, when he retired to work with the Chinese at the Hong Kong Baptist Theological Seminary.

Dr. Elbert H. Walker was elected the second President in 1964 but his service was cut short by his untimely death in 1965. Dr. Walker initiated the establishment of the administrative organization of the school.

In 1965, Dr. Grover F. Tyner, Jr. was named the third President. He served until his retirement in 1987 and became President Emeritus. Dr. Paul P. Johnson was elected as the fourth President in 1987 and resigned in 1989. Rev. Robert N. Nash, Sr., was inaugurated as the fifth President in October 1989 and retired in May 1991. Dr. D. Leslie Hill was appointed as the sixth President in November 1991. He served until 1998. Dr. Alfredo G. Saure was elected as the seventh president in 1997 and assumed his post on June 25, 1999 until 2006. He is the first Filipino President Emeritus. Elected last March 9, 2006 and installed July 7, 2006 as the eighth president is Dr. Joyce J. Abugan. She is the first woman to serve in this post, serving until December 2012.

In September 2012, the Board of Trustees named and installed Dr. Armando M. Canoy as the ninth president. He is the current president of the seminary.