The origins of the devotion to Our Lady of San Juan del Valle began in San Juan de los Lagos, a Mexican town founded after the Spanish conquest. Here, Spanish missionaries installed an image of the Virgin Mary in the town's church to assist parishioners in their devotion. According to the church, in 1623, a family of acrobats were performing in town when their youngest daughter lost her balance and fell to her death. However, when the image was placed over her body, the child appeared to return to life. Considered a miracle by the church, the image became recognized throughout Mexico as Our Lady of San Juan.

The devotion carried into the U.S., where, in 1949, Reverend Jose Maria Azpiazu of the San Juan, Texas parish received permission to foster a devotion to Our Lady of San Juan. The Reverend commissioned a reproduction of the venerated statue inspired by the original image residing in San Juan de Los Lagos and placed it in the San Juan Chapel. A new church and shrine, built and dedicated to the Virgin of San Juan in 1954, followed. Sixteen years later, during a Mass attended by 50 parishioners and 50 priests, with 100 school children in the church's cafeteria, a small plane crashed into the roof of the shrine and exploded, destroying the shrine. Remarkably, no one but the pilot died in the conflagration and the statue, along with the sacrament, were rescued from the flames.

Today, the rebuilt shrine has achieved international recognition and, in 1999, Pope John Paul ll bestowed its title as Basilica.