The history of APTS started when the Far East Conference of the Assemblies of God that met in Hong Kong in 1960 strongly urged the establishment of an advanced school of theology to serve the entire area of the Far East Region. Several years of careful planning followed, directed largely by Maynard Ketcham, field secretary for the US Assemblies of God for the Far East. The school was established in 1964 as the Far East Advanced School of Theology (FEAST), with Harold Kohl as the founding president. The first building was constructed on the compound of Bethel Bible Institute in Manila, Philippines. This facility served the school until 1986 when the campus was moved to its present location in Baguio City, Philippines.

The curriculum of the school was originally structured to accommodate Assemblies of God ministers and Christian workers who had completed only a three-year Bible institute program. Bachelor of Arts degrees in Biblical Studies and Religious Education (four-year degrees), and a five year Bachelor of Theology degree were offered. In 1978 the program was expanded to include Masters degrees in Biblical Studies and Christian Education, and the Master of Divinity degree program was added in 1982.

In 1989 the Bachelor of Arts programs began to be phased out. In 1985, the property was purchased in Baguio City, Philippines, to provide a permanent campus for the school. Operations were moved to the new site in October 1986. In the years that followed, a number of buildings were erected on the new campus to house the growing student body and academic programs.

The name was changed from Far East Advanced School of Theology to Asia Pacific Theological Seminary (APTS) in 1989 to better reflect the nature of the school in offering graduate degrees in theology. That same year the Master of Divinity degree was accredited by the Association for Theological Education in South East Asia (ATESEA). Their accreditation was renewed in 2003. In the same year Asia Pacific Theological Association (APTA) granted accreditation and in early 2000 accreditation was received from the Asia Theological Association (ATA).

Both the APTA and the ATA accreditation were renewed in 2021. The ATESEA accreditation is due for renewal in 2025. From 2000-2002, several post-graduate programs were added, including the Th.M. in Pentecostal/Charismatic Studies (2000), which was replaced with the MTh (2009), and the D. Min in Pentecostal/Charismatic Spirituality (2002). In addition to the classes offered on the campus of APTS, courses are taught in extension centers in several Asia Pacific countries. More than 3,000
students have studied in APTS extension classes.