According to Christian tradition, the Virgin Mary appeared in Zaragoza on January 2, 40 on a column, known as the Pilar. As a result of this belief, it is said that the Virgin Mary asked for a chapel to be built in that place, a work that the apostle Santiago would have carried out together with the first converts of the city.

There is no archaeological or documentary evidence of that first chapel, but there is evidence of the existence, in the ninth century, of a church dedicated to Santa María on the same site, around which a Mozarabic community was organized.

After the conquest of Zaragoza by Alfonso I of Aragon in 1118, the temple was in ruins, so the bishop Pedro de Librana had to condition it for worship. Subsequently, construction began on a Romanesque church, which was not completed until the 13th century. The old chapel of Pilar dates from that period, documented in 1240 as an independent place of worship. In 1297, a papal bull confirmed the veneration of the Pilar and the consolidation of the cult of Santa María del Pilar.

At the end of the 13th century and until 1515, a new temple was built in Gothic-Mudejar style, which included a carved choir and the main altarpiece commissioned to Damian Forment. The state of this temple is known thanks to sketches, views of the city and notarial documents of the time. The old chapel was maintained until the reforms of the 18th century.

In 1670, under the impulse of Juan José de Austria, the construction of the current baroque temple began, initially directed by masters from Zaragoza and continued by the royal architect Francisco de Herrera el Mozo. In 1730 the enlargement was completed, reaching its present dimensions. Between 1754 and 1765, Ventura Rodríguez designed the new chapel of the Virgin and introduced modifications in the interior decoration, giving it a more sober style, closer to the neoclassical taste.

The characteristic silhouette of domes and towers was completed between 1796 and 1872, although the corner towers were not finished until 1961, giving the church its definitive appearance.