The Santo Niño de Cebú image was originally produced by Flemish artisans, according to a hagiography, based on a vision of Teresa of Avila a mystic of the 16th century.
In early 1521, the Portuguese explorer Ferdinand Magellan, in the service of Charles V of Spain, was on his voyage to find a westward route to spice islands. In April 7, 1521, he landed in Limasawa, Southern Leyte, and met local ruler named Raja Kulambu, who introduced him to the ruler of Cebu Island named Rajah Humabon (some records refer to him as Sultan Humabon) and his chief consort, Hara Humamay. On April 14, 1521, Magellan presented them with three gifts: a cross, an image of the Blessed Virgin Mary and Santo Niño as a part of their baptism, and a strategic alliance for territorial conquest. As the host ruler adopted the Catholic faith, he took the Christian name of Carlos (after Charles V), while Humamay was christened Juana (after Joanna of Castile, Charles' mother). According to Pigafetta – Magellan's companion and memoir writer, along with the ruler, about 500 males there, along with the Sultana and 40 women were also converted by Father Valderrama. At the ceremony, for example, the Raja Kulambu of Limawasa also converted and was renamed as Don Juan, while his Muslim captain was renamed Don Cristobal.
A few days after the baptism, Magellan undertook a war expedition on the behalf of the newly named Carlos, attacked Mactan Island, burning down hamlets who resisted. The residents led by Lapu Lapu defended Magellan's attack with force, and Magellan died on 27 April 1521 in the Battle of Mactan, about three weeks after he had arrived in Philippines. After Magellan's death, his Spanish colleagues left.
The next Spanish expedition arrived on April 27, 1565, again to gain a foothold for a colony to trade spices, and this was led by Miguel López de Legazpi. He attempted a peaceful colonization, but these efforts were rejected. He opened fire on Cebu and burnt the coastal town down destroying 1500 homes and possibly killing 500 people. In the ruins of this destruction, the Spanish mariner Juan Camus found the image of the Santo Niño in a pine box. According to the local legend, the survival of the statue was seen as a sign of miracle by the colonizers, and ever since it has been believed to have miraculous powers.
The image of the Santo Niño is the oldest surviving Catholic relic in the Philippines, along with the Magellan cross. A church to house Santo Niño was built on the spot where the image was found by Juan Camus. The church was originally made out of bamboo and mangrove palm and claims to be the oldest parish in the Philippines. It was reconstructed later, and Pope Paul VI elevated it to the status of Minor Basilica on its 400th anniversary (Spanish: Basílica Menor del Santo Niño).