On April 7, 1521, the Portuguese navigator Ferdinand Magellan arrived and planted the cross on the shores of Cebu, claiming the territory in the name of the King of Spain. He presented the image of the child Jesus, the Santo Niño, as baptismal gift to Hara Amihan, wife of Rajah Humabon. Hara Amihan was later named, Queen Juana in honor of Juana, mother of Carlos I. Along with the rulers of the island, some 800 natives were also baptized to the Christian faith. At the moment of receiving the image, it was said that Queen Juana danced with joy bearing the image of the child Jesus. With the other natives following her example, this moment was regarded as the first Sinulog.

This event is frequently used as basis for most Sinulog dances, which dramatize the coming of the Spaniards and the presentation of the Santo Niño to the Queen. A popular theme among Sinulog dances is Queen Juana holding the Santo Niño in her arms and using it to bless her people who are often afflicted by sickness caused by demons and other evil spirits.

The word Sinulog comes from the Cebuano adverb sulog which is "like water current movement," which describes the forward-backward movement of the Sinulog dance. The dance consists of two steps forward and one step backward, done to the sound of drums. The dance is categorized into Sinulog-base, Free-Interpretation. Candle vendors at the Basilica continue to perform the traditional version of the dance when lighting a candle for the customer, usually accompanied by songs in the native language.

The Sinulog dance steps were believed to originate from Rajah Humabon's adviser, Baladhay. It was during Humabon's grief when Baladhay was driven sick. He then ordered his native tribe to bring Baladhay into a chapel where the Santo Niño was enthroned. Moments later, surprisingly, Baldhay was heard shouting, and was found dancing with outmost alertness. Baladhay was questioned as to whether why was he awake, and was shouting. Baladhay explained that he found a small child, pointing to the image of the Santo Niño, on top of him, and trying to wake him up. He, at great astonishment, scared the child away by shouting but couldn't explain why he was dancing the movements of the river. Up to this day, the two-steps forward, and the one-step backward movement dance is still used by the Santo Niño devotees believing that it was the Santo Niño's choice to have Baladhay dance what the holy child wants them to dance.