Back in April of 2014, the Manila Cathedral was finally re-opened and, interestingly enough, the CBCP newsite dubbed it as the “mother of all Philippine churches” for reasons being an important episcopal see and the structure’s antiquity. Before the news, blogs and others on the internet assumed this title. What’s more fascinating is the Basilica del Sto. Niño and the Cebu Cathedral preceded other Christian structures in the Philippines (Nestorian Christianity not included).
Before becoming the cathedral now, the Cebu bishop’s see was primarily an ordinary church built by Miguel Lopez de Legazpi and Fr. Andres de Urdaneta. Bishop Pedro Agurto, O.S.A., (the first Cebu diocesan prelate) chose the structure as his see in 1595. On the same day of the Cebu Cathedral’s foundation (April 1565), the Augustinian church and convent (also the first ever convent in the archipelago) was established on the very spot the image of the Sto. Niño was found. The Cebuana Anthropologist Astrid Sala-Boza, when settling the issue where the Holy Image was found (Basilica del Sto. Niño vs. San Nicolas de Tolentino Church), she demonstrated that the Cebu Cathedral was also the church established in 1565. 
In 1965, during the celebration of the 400th anniversary of evangelization (not Christianization) in the Apostolic Letter Ut Clarificetur, Pope Paul VI described in Latin the genesis of Christianity and called the church enshrined the Sto. Niño not only the “mother” of all the future churches in the archipelago but also its “head”! 
Let me be clear, this is in no way minimizing the importance of the Manila Cathedral–far from it. Manila is one of the most influential and important episcopal sees. However, we have to look at the eminence of the Basilica del Sto. Niño and remember the “mother and head of all churches” in the country is canonically under the equally historical Cebu Cathedral, thus, consequently making Cebu the primatial see of the Philippines.
1. For perusal on the subject: Sala-Boza, Astrid, “The Contested Site of the Finding of the Holy Child: Villa San Miguel or San Nicolas (Cebu El Viejo),” Philippine Quarterly of Culture Society 34, (2006): 232. Also available in the University of San Carlos Publication
2. The Christian faith started in 1521 at the arrival of Ferdinand Magellan and Fr. Pedro Valderrama. While it’s true there was an evangelization transpired in 1521 materially, the formal endeavor happened in 1565. In the year 2021, the Philippines will celebrate half a millennium of Christianity.
3. “mater et caput… omnium ecclesiarum Insularum Philippinarum.”