Long before the Papal visit of the Holy Father, Pope Paul VI to the Philippines in the year 1970, the proposed plan to divide the parochial population of Sto. Niño Parish has already received the initial approval from the Cardinal of Manila, the late Rufino Santos.  This idea began in December 1968. It was the Papal Nuncio, Msgr. Carmine Rocco who continued the discourse and carried out the initiative to its concrete realization.  During that time, there were only three priests giving services at Sto. Niño Parish, making it hard and impossible to meet the growing needs of the parishioners, especially the poor in the squatters area. 
     In the latter days of November 1970, the Cardinal agreed to form two new parishes in the communities within the vicinity of the port of Manila in Tondo. One parish was established at the entry of the North Harbor area, to be called Our Lady of Peace and Good Voyage, entrusted to the Augustinian Recollects. The other parish is at the extreme end of the harbor (Magsaysay Village) giving parts of the territory of the parishes of Don Bosco and Sto. Niño, to be called the San Pablo Apostol Parish, in memory of the coming visit of Pope Paul VI, entrusted to Fr. Bruno Piccolo and Fr. Joseph Vancio, PIME Fathers.  Their presence in Tondo within the squatters area, the poorest of the poor, was a clear evangelical choice to bring the message of hope, light, and truth; to share their life, their sufferings, and their insecurities.  It was to follow the path that God has shown in the history of salvation, to take as His own, the poor, and prepare for them a kingdom.  In this place, they discovered their mission, where they can witness that the church loves the poor.  Early in December 1970, the two PIME fathers wasted no time to find a place of their own, where they began a program of spiritual and material assistance to the community. They were able to purchase a small bungalow on a 500 sq.m. lot, located at Emilio Jacinto St., Magsaysay Village, and eventually constructed a small parish church, a meeting center, and a residence. It was blessed and dedicated on Christmas Day, 1972 by the Most Rev. Carmine Rocco.
     It was in early January 1971, that the boundary for the new parish of San Pablo Apostol was set up.  It extended the whole area from Capulong St. to Vitas Tenement.  At present, the boundary extends from Herbosa Pritil until Vitas Tenement.
     As years went by, various groups of PIME Fathers came and went to the San Pablo Apostol Parish until  l979, which became the most memorable event for the parishioners of Nepo-Velasquez.  It was the year that the new chapel of San Pablo was built, with much appreciation to the combined efforts of Fr. Gianluigi Colombo, who was in charge of the place during that time and the parishioners themselves. It became San Pablo-B.  
     In 1981, the PIME Fathers left Tondo, after almost ten years of apostolate to the parish.  After the PIME Fathers, came the Congregation of the Society of St. Columbans, in the persons of Fr. Sean Connaughton for Magsaysay Village and Fr. Patrick O’Herlihy for the church in Neomuceno-Velasquez.  Fr. Pat O’Herlihy was able to build the San Pablo Apostol Parish Center with free medical and dental care for the sick poor people.  
     In July 1989, the Society of St. Columbans decided to leave Tondo, to usher in the Canossian Fathers, Fr. Stefano Arnone, who was installed as Parish Priest in December 1989, and Fr. Giovanni Gentilin, as Asst. Parish Priest.  In July 1997, Fr. Giovanni Gentilin, FdCC officially installed as Parish Priest and therefore the parish traversed under his leadership until July 2007,  So far, the most valuable program ever initiated by the parish is the SCHOLARSHIP PROGRAM, giving educational assistance from pre-school up to college to deserving children in the parish community. From July 2007, Fr. Carlo Bittante, FdCC succeeded as parish priest up to the present. The main initiative for the actualization of peoples’ dream of Tondo to build a new church was started with Fr. Carlo’s proposal, and optimistically pushed through by the PPC and the community of San Pablo Apostol, Tondo Manila.     
     On October 4, 2007, the Archdiocese of Manila was able to partially acquire a part of a hectare of land and received as a gift the remaining greater part of the 12,000 sq. m. from the Ayala Land Corporation. A hectare (10,000 sq. m.) was made available by his Eminence, Gaudencio B. Cardinal Rosales, then Archbishop of Manila, to the Parish meant to be the new center of Parish activities.
     Thanks to the help of an Italian foundation and to the many friends and benefactors, we were able to finish the construction of the first project: the “Youth Formation and Social Center” composed of two buildings – a Covered Court and a YouthCenter. On October 3, 2010, it was blessed by Cardinal Rosales. 
     The groundbreaking for the construction of the new Church building was held on January 22, 2012, during the Parish Fiesta celebrated by the new Archbishop of Manila, Archbishop Luis Antonio G. Tagle. Since then, different initiatives and projects are being done to continue building our dream Church for the parishioners of San Pablo Apostol in Tondo.