[2] Pope John Paul II raised the shrine to the status of Minor Basilica via the pontifical decree Signum illud Sanctuariumque on 15 July 1982.

The parish was founded in 1578 by Franciscan friars John Baptist Lucarelli of Pesaro, Italy, and Sebastián de San Francisco of Baesa, Spain.

The original church was constructed with native materials, nipa and bamboo (in Barangay Nagreban or Nagrugcan) under its patron saint Francis of Assisi.

The church was finished and consecrated as a Marian shrine on December 8, 1978, by Cardinal Sebastiano Baggio coinciding with the quadricentennial of the Christianization of Agoo.

Cardinal Agostino Casaroli's re-script dated July 15, 1982, signed for Pope John Paul II, granted Bishop Salvador Lazo's petition elevating the Shrine of Our Lady of Charity to a minor basilica.

A pipe organ in the choir loft watches the craved chandeliers dotting the middle aisle, 2-tiered and carved or made of Filipino mahogany, demonstrating the rich heritage and vast culture of Agoo.

The basilica has preserved stone blocks dragged from the original church amid its charming garden, an old wishing well and the interior mural "The Second Coming of Christ" (by Rey Gimeno).

[8] The 17th-century wooden statue of Our Lady of Charity was first venerated and enthroned in Bantay, Ilocos Sur and brought to Agoo by an Augustinian priest.

The crowned head of the original statue is made of baked clay covered with a polished coat of fine white powder.

[9] Bishop Victorino C. Ligot of the Roman Catholic Diocese of San Fernando de La Union filed the ecclesiastical petition to the Sacred Congregation for the Sacraments and Divine Worship in Rome for the canonical coronation of the statue, with the collaboration of Jose D. Aspiras, who helped restored the belfry, but was denied with a letter issued from the Congregation dated April 4, 1971, which in turn, was suggested to crown the image by the authority of the bishop instead.

This distinction was announced on June 5, 2024, through a circular released by the Roman Catholic Diocese of San Fernando de La Union regarding the approval of the petition.