As early as the 1600's, the Roman Catholic Church has paid particular attention to the needs and aspirations of the Filipino-Chinese faithful.

The evangelization of the latter, through the efforts of the Spanish clergy, was foremost in the minds of the princes of Rome, who did their best to assimilate the Filipino-Chinese in faith and culture.

But it was not until 1928 when under the authority of His Holiness Pope Pius XI, the first official Filipino-Chinese parish was organized in Binondo within the aegis of then Archbishop of Manila Michael O-Doherty.

The burgeoning growth of the Filipino-Chinese community, coupled with the need to expand geographically, made imperative the canonical erection of more Filipino-Chinese parishes, so that the original Binondo Parish gave birth to three more: St. Jude Parish of San Miguel, Mary the Queen Parish in San Juan and St. Peter the Apostle Parish in Paco, Manila. The authority for such expansion was granted by the Sacred Roman Consistorial Congregation (July 23, 1954). Thus, St. Peter the Apostle Parish was born on September 20, 1954.

Msgr. Juan B. Velasco, appointed by His Holiness John XXIII as Spiritual Head of the four parishes, became the National Director of the Chinese Apostolate in the Philippines.

By the time the Papal Order was to be implemented in Canonigo, Paco, Manila, a church was already standing – St. Joseph's under Fr. Louis Fossion, CICM. This church was renamed as the St. Peter the Apostle Church.

The geographical limits of the parish were defined as "in the North, by the Pasig River, running from Manila Bay in the west, to the boundary line of the Rizal Province to the East and South." The Canonical Order stated that "all the Chinese inhabitants within those limits will constitute the members of the new parish." Thus, the following were now part of the parish: Sam Fernando de Dilao, Sta. Ana, San Andres, Singalong, Malate, Asuncion de Nuestra Señora, San Vincente de Paul, Intramuros, Ntra. Señora de Pañafrancia, Pandacan, Ermita and San Isidro de Labrador (Parte). Likewise, the order granted the parish "the privilege to keep habitually the Blessed Sacrament, to possess a baptismal font, to administer all sacraments" and other rights of a parochial church.

One of the earliest benefactors of the new parish were Mr. and Mrs. Melquides Virata and Conception Andrea Gonzales, who allowed the parish to use the 650 sm. m. Lot used by the St. Joseph church for free. Through the efforts of Fr. Fossion and the Chinese community in the area, the parish was able to purchase the adjoining 1,713 sm. m. lot on May 18, 1956 from Mr. And Mrs. Fortunato de Leon and Juana Gonzales to build a new church, rectory and parochial school. The smaller lot formerly being leased to the parish for free was also purchased on October 22, 1958.

On September 17, 1958, Rev. Fr. Jacques Mussen (better known as Fr. James) came to Manila as the new parish priest. He completed the church, but after 15 years as parish priest, he fell ill and had to return to Belgium.

Fr. Joseph Liu took over as parish priest in 1973. On December 22, 1974, a diocesan priest named Fr. Vincent Liu arrived from the United States as the next parish priest. Sensing the need for an institution that would look after the Catholic education and infusion of the Chinese culture in the Filipino-Chinese youth, Fr. Liu saw the need for a school.

Support for his vision came from His Eminence Jaime Cardinal Si, Archbishop of Manila, and His Excellency Msgr. Juan B. Velasco, OP. Thus was born St. Peter the Apostle School and on the first anniversary of his arrival in Manila, the school received its permit to offer classes from the Bureau of Private Schools. June 14, 1976 marked the opening of classes with the enrolment of 101 pupils for the Nursery, Kinder and Grade 1 levels. On November 6, 1977, ground breaking ceremonies were held for the construction of a new school building. On February 4, 1978, Cardinal Sin and Msgr. Velasco inaugurated the building.

On August 1, 1981, Fr. Francis Chin took over from Fr. Liu, who served the parish for seven fruitful years. He became the parish priest and school director with the assistance of Fr. Thomas Chao. Fr. Francis' administration and resourcefulness endeared him to the parish Filipino-Chinese community, and was invested the title of Monsignor on April 14, 1985 by His Holiness John Paul II. A year later, the Kindergarten building named after is benefactor Mr. Eduardo Cojuanco) was completed along Peñafrancia Street. It was inaugurated on March 16, 1986 by His Eminence Cardinal Sin.

On August 25, 1986, the St, Peter the Apostle Parish was granted the status of Territorial Parish. This meant that the former personal parish of the Filipino-Chinese community became a legitimate geographic parish for the needs of all the faithful in Paco, P.M. Guanzon and Quirino Avenue.

To attend to the various outreach programs, Fr. Vic Virtudazo joined the parish on June 1993.

On August 23, 2003, the majestic St. Peter the Apostle Church was blessed by His Eminence Cardinal Sin after only one year of construction.

On July 25, 2012, Msgr. Noly A. Que, LRMS, MBA, PhD became the new parish priest and school director. He was installed by His Excellency Most Rev. Luis Antonio Tagle, DD last August 19, 2012 on the occasion of his 14th Sacerdotal Anniversary. Msgr. Noly, together with his fellow priest-administrators Fr. Roberto Fabillo, LRMS, Rev. Fr. Simon Zhu and Rev. Fr. Junerl Salugsugan, continued the legacy of Msgr. Chin to build up the parish both spiritually and physically. At the end of 2012, construction began for a new parish office to better serve the parishioners. Soon, a new parish rectory will be constructed.