The Parish of San Isidro Labrador in San Fernando town, Cebu was established as an independent parish by the Augustinians through diocesan decree on 19 June, 1858 with Fray Fernando Sanchez as the first parish priest. The present church was designed by Fernando Escondrillas, Spanish architect and engineer who drew the plans for the church in 1870. The edifice was finished in 1886.
The church is made from cut coral stones, like most of the coastal churches in the Visayas. It is one of a few edifices in the neogothic design and was chosen by Fray Emiliano Diez who considered the Gothic style as serious and worthy of the church to be built. As one might notice, the twin belfries seems incongruous with the overall structure. These were actually built later in the 20th century and are made of cement.
During World War II, it was spared from the damages of war, unlike many of the churches in Cebu, Talisay Church for example. The interior was renovated in 1972. The separate two storey, coral stone kumbento was turned into a school in 1945.