The church has been a pilgrimage site for two patron saints of Gapan and also of Nueva Ecija; the Three Kings, and the Divina Pastora (Divine Shepherdess).

Situated across the Rio Chico, Gapan was originally bounded by Manicling, San Miguel de Mayumo and the Cordillera mountains.

In 1704, Governor General Domingo de Zabalburu ordered that all Chinese living in the missions of Bongabon, Santor, Carranglan and Pantabangan transfer to Gapan.

The exterior of the church is plain while its interior formerly has a central retablo with niches dedicated to the Epiphany of the Lord and to the La Virgen Divina Pastora.

It was replaced with a modern style sanctuary dominated by a huge image of the Crucifixion, arguably the largest in the province of Nueva Ecija.

Prominently displayed on the left retablo is the original miniature image of the Virgen Divina Pastora which was donated by the Valmonte Family in 1986.

[9] On December 19, 1963, Pope Paul VI approved the canonical coronation of the image of La Virgen Divina Pastora.

[10] Since the original image is privately owned, a church-owned replica was used for the coronation ceremony, which was presided by the first Bishop of the Diocese of Cabanatuan, Most Rev.

The original image of the La Virgen Divina Pastora was eventually donated to the Parish of the Three Kings with the declaration of the church as a national shrine on April 26, 1986.

[11] A Pontifical Mass was held on April 26 to solemnly declare the shrine as a basilica, presided by the Apostolic Nuncio to the Philippines, Archbishop Charles John Brown, and concelebrated by twenty bishops and a dozen Catholic priests.