In 1755 the first structure of wood and thatch was built on this site by the Augustinian friars under the patronage of San Fernando III, King of Castile.

The round majestic dome rising from the rotunda of the transept is reminiscent of the Baroque style with some Renaissance elements.

President Emilio F. Aguinaldo and his cabinet viewed the Philippine Revolutionary Army from the windows of the convento on October 9, 1898.

[citation needed] On orders of Gen. Antonio Luna, the Philippine Revolutionary Army burned the church and convento on May 4, 1899.

[citation needed] The church was destroyed by fire again in 1939, and restored by Pampango Architect Fernando H. Ocampo in 1948.

In 1948 the church was elevated to Cathedral when it became the seat of the Diocese of San Fernando, canonically created by Pope Pius XII.