This occurred after the country opened to Protestant American missions in 1898, following Spain's transfer of the Philippine islands administration to the United States.

CPBC is associated with the American Baptist Foreign Mission Society (now International Ministries) and played a key role in establishing the Jaro Evangelical Church, the first Baptist church in the Philippines outside Manila.

The Convention of Philippine Baptist Churches has its origins in a foreign mission of the American Baptist Missionary Union on the island of Panay in February 1900,[1][2] when the Philippines islands was opened to the Evangelical missions after it was ceded to the United States administration.

Eric Lund, a Swedish Baptist minister working under the auspices of the American Baptist Foreign Mission Society and one of the founding fathers of the Jaro Evangelical Church, translated the entire Bible into Hiligaynon, and the New Testament into two other dialects.

CPU's earliest forerunner, the Central Philippine University College of Theology which was established four months earlier than the university's second precursor, the Jaro Industrial School, is the first Baptist theological seminary in the Philippines.

Central Philippine University's official student governing body, the CPU Republic (Central Philippine University Republic), is the oldest student government in the South East Asia.