In 1977 the General Board of the Church of the Nazarene approved a plan to establish a graduate Seminary to serve the Asia and Pacific region of the church. The particular needs of the church in this part of the world demanded this. Dr. Donald Owens, Professor of Missions at Nazarene Theological Seminary in Kansas City and formerly a missionary to Korea, was elected to head the new seminary, which would become the first master's-level theological institution of the Church of the Nazarene located outside the United States.

In 1979, the church purchased a site in Taytay, Rizal, Philippines. Formerly an orphanage, the location consisted of ten acres with 22 wooden frame buildings. The proximity of the location to Manila was a deciding factor, as leaders hoped that the cosmopolitan setting would provide models for evangelism for the other cities of Asia and the Pacific. The Church of the Nazarene had directed its attentions to Metro Manila only a few years earlier.

Beginning in 1980, extension seminars were held involving several NTS professors as well as Rev. Angelito Agbuya, pastor of the Angeles City, Philippines, Church of the Nazarene. Students represented various countries in the region. Meanwhile, Dr. Owens became Director of the Asia Region and moved to Manila. As extension classes were held over the next few years, general church leaders concluded that the new Seminary should become autonomous from NTS. In preparation for the opening of a residence program, Dr. Owens searched for faculty members and initiated construction of an administration and classroom building,the ground breaking ceremony for which was held in January, 1983. Other buildings on the campus were renovated for student and faculty living. The Commission on Immigration and Deportation, Department of Justice, Republic of the Philippines, gave its approval for APNTS to begin as an educational institution for non-immigrant students.

Finally, regular classes began on November 14, 1983. The faculty included Dr. Owens, Dr. Agbuya, Dr. and Mrs. Ronald Beech, long-time missionaries in the Philippines, and Dr. Floyd Cunningham. The Seminary was formally dedicated and the faculty installed on January 15, 1984.

In April, 1984, Dr. E. LeBron Fairbanks, formerly Academic Dean of European Nazarene Bible College and at the time teaching at Southern Nazarene University, was elected President of the Seminary. He began serving in the office in July, 1984, and he and his family moved to Manila later that year.

In 1987, the seminary received its permit to operate from the Philippine government's Department of Education, Culture and Sports (now the Commission on Higher Education), and full recognition from the same Department came on June 13, 1988. Accreditation for degree programs was also granted by the Asian Theological Association (ATA) in 1988, and by the Association for Theological Education in South East Asia (ATESEA) in 1991.

Meanwhile, the library was strengthened with the addition of several important collections centering on Wesleyan and holiness studies, and came to number over 30,000 volumes by 2003.

At the same time, extensive renovation and building programs on campus continued under the guidance of Rev. Gordon Gibson, who served as Campus Development Coordinator from 1984 until 1992, Mr. Terry Sanders, 1992 to 1998, Mr. Greg Taylor, 1998 to 1999 and, again, from 2004, Mr. David Hendrix, 1999 to 2004.

The faculty was strengthened in succeeding years. In addition to current faculty members: Dr. Ronald Beech taught Biblical Studies from 1983 to 1992; Dr. James Edlin, Old Testament, 1985 to 1988; Dr. Wilfredo Manaois, Christian Education, 1986 to 1999; Dr. Donald Stults, Missions, 1987 to 1991; Dr. Dean Flemming, New Testament, 1987 to 1992, and 1993 to 1997; Dr. Lourdes Manaois, Christian Education, 1987 to 1991, and 1993 to 1999; Dr. M. Robert Fraser, Theology and Church History, 1988 to 1992; Prof. Janice Nielson, Christian Education, 1990 to 2001; Dr. Abraham Athialy, Pastoral Ministry, 1992 to 1998; Dr. Roderick Leupp, Theology and Christian Ethics, 1992 to 2000; Dr. David Kelly, Biblical Studies, 1993 to 1994; Dr. Dwight Swanson, Old Testament, 1995 to 1997; Prof. Joven Laroya, Christian Education and Pastoral Ministry, 1999 to 2001; Dr. Stanley Clark, Christian Education, 2000 to 2004; Dr. Hitoshi (Paul) Fukue, Theology and Christian Ethics, 2001 to 2007; Prof. Mitsuko Fukue, Christian Communication, 2001 to 2007; Dr. Gilbert Montecastro, Biblical Studies, 2002-2006; Dr. Oh Won Keun, Old Testament, 2004 to 2007. The seminary also has used a number of distinguished adjunct and visiting professors.

Trustees chose Dr. John Nielson, Vice-President of Eastern Nazarene College, and formerly a missionary to Denmark, as President. He and his wife Janice Nielson settled in Manila in February 1990. Dr. Nielson taught in the area of Pastoral Ministry, and Mrs. Nielson in Christian education. They served until 2001. In the Nielsons’ honor, in April 2003 the Seminary dedicated a major building on campus, the Nielson Center for Education and Evangelism.

In January 2003, the Board of Trustees chose Dr. Hitoshi (Paul) Fukue, who had been serving on the faculty since 2001, as President. Before coming to APNTS in 2001, Dr. Fukue had served for many years as a pastor in Japan, and had served as President of Japan Christian Junior College. He was inaugurated as President in April 2003. He resigned from the presidency in 2007 to accept a pastorate in Japan.

Floyd T. Cunningham, as Academic Dean, served as Officer-in-Charge during the sixteen months between the presidencies of Dr. Nielson and Dr. Fukue, and again following the resignation of Dr. Fukue.

In 1993 the Asia-Pacific region established a media center on campus, the Fairbanks Media Center. This enabled APNTS to begin a communication major within the MA (RE) program. In 1996 the Commission on Higher Education gave recognition to a Master of Arts Christian Communication degree program. The program has grown into the Fairbanks School of Communiation, name in the honor of the second President of APNTS.

In 1996 the faculty publication of the Mediator began. The Philippines' CHED required graduate schools to issue a journal. The Mediator seeks to communicate to the APNTS constituency and graduates. It provides a forum and vehicle for faculty publications and seeks contributions from graduates and other interested parties.

Increased attention to English as a Second language came with the appointment in 1997 of Beverly Gruver who had been a high school English teacher and missionary in South America, and reeducated herself in teaching English as a second language, finishing PhD coursework at the University of Kansas in 2004.

In 2002 the Master of Science of Theology program was developed to help prepare graduates for teaching courses at undergraduate Bible and Theological Colleges and for further graduate work by requiring a thesis. In 2004 the Owens School of World Mission was inaugurated as a resource for training for mission preparation.

More than 300 graduates of APNTS have gone on to pastoral, teaching, missionary, administrative and many other forms of ministry in various countries, including: Australia, Bangladesh, Canada, Hong Kong, India, Indonesia, Japan, Kenya, Myanmar, New Zealand, Papua New Guinea, the Philippines, Samoa, South Africa, South Korea, Taiwan, Thailand, Ukraine, and the United States.