The church was organised by missionaries Vince and Lucy Apostol of the Christian Reformed Church in North America. The mission started in 1962 when the Christian Reformed World Mission begun planting churches in Negros Island. In 1976 the denomination was officially organized with three congregations. By the 1990s the church had 20 congregations and mission churches. Churches were organised into five classes. A synod was formed in 1983. By 1990 it had grown to 25 organized churches and 20 church plants. Now the church has over 50 congregations and 5,000 mermbers.
The Reformed Institute of Theology was founded in 1969 to provide theological training of the Philippian Christian Reformed Church. On January 1970 the opening ceremony was held with 50 men and women. On June 1975 it become the Genevan Reformed Seminary. Finally it become the Christian Reformed Seminary and Bible Institute. It is a growing institution, located in Bacolod City, Negros Occidental. The bible school in Bacolod City is non-operational as of this time.