In the year 1989, May 19, Rev. Moon-Sun Lee accompanied by his wife Mrs. Young-Seon Lee and children, a son, Ku-Yeon Lee, and a daughter, Seong Yeon Lee landed in Dumaguete City, Negros Oriental. They were from the Presbyterian Church of Korea. Rev. Lee enrolled in the Divinity School at Silliman University and finished his Masters of Theology course, adding to his foundational theological course taken in South Korea.
The visionary Rev. Lee saw mission field in the faces of Filipino young people. The high costs of college education practically relegate them to the marginalized sectors. With the help of friends and churches in Korea, Rev. and Mrs., Lee established this mission in the name of the Presbyterian Church Inc. which was registered with the Security and Exchange Commission in 1992.
The college started offering the Course, Bachelor of Arts in Theology (AB-Theology) under the Recognition from the Commission on Higher Education. Few years later, Education and other courses were also offered. The LORD continues to bless the Presbyterian Theological College that in 2008, The Pre-School, Elementary School and Junior High School Departments were also duly recognized by the Department of Education. In 2016, the Senior High School Department of the Presbyterian Theological College was also Recognized by the Department of Education.