It was established by the Episcopal Church of the United States (Protestant Episcopal Church in the United States of America) in 1901 by American missionaries led by Charles Henry Brent, who served as the first resident bishop, when the Philippines was opened to Protestant American missionaries.

The current Prime Bishop is Brent Harry Alawas, serving until March 2025 when he will be succeeded by Nestor Poltic.

The first Episcopal Church worship service conducted for Filipinos took place on December 25, 1898, Christmas Day.

In April 1899, Hugh Nethercott and James Smiley of the Brotherhood of St. Andrew arrived to assist the American chaplains in their work.

Appointed to oversee American church work in the Philippines and later, bishop-in-charge, he held worship services in the home of a British couple.

The first baptisms in Manila were performed in 1900 by U.S. Army Chaplain John Marvine when he baptized three Amoy-speaking nationals and 12 more by the end of the year.

From being a mere outreach chaplaincy of the Episcopal Church chaplains of the U.S. occupation armed forces in the Philippines.

Temporarily placed under the oversight of Bishop Frederick Graves, it was officially created as the Missionary District of the Philippine Islands of the Protestant Episcopal Church in the United States (PECUSA) by the PECUSA General Convention held in San Francisco on October 4–11, 1901.

As a consequence, his missionary focus was in those parts of the islands that had not previously been evangelised, in particular, in the mountain provinces and in Mindanao.

It was at that time that part of the Cathedral congregation formed the Church of the Holy Trinity, now located in the upscale village of Forbes Park, Makati.

In addition to children of expatriates, a large number, if not the majority, of enrollees in the Brent Schools are Filipinos from well-to-do families.

With regard to starting missionary work and establishing a church for and among the unchurched, Bishop Brent was against proselytization.

At that time, most non-Christians in the Philippines were migrant Chinese in Manila, indigenous peoples in the North and in the South as well the Muslims in Mindanao.

In time, the government was able to establish public schools, hospitals, and rural health centers for these communities.

As a result, this Church phased out some of its schools and clinics in favor of the government providing such basic services needed by these communities.

The Episcopal Church in the Philippines maintains the historic threefold ministry of bishops, priests, and deacons.