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The Rajahnate of Cebu was a native kingdom which existed in Cebu prior to the arrival of the Spaniards. It was founded by Sri Lumay otherwise known as Rajamuda Lumaya, a half-Malay, half-Tamil prince of the Chola dynasty who invaded Sumatra in Indonesia. He was sent by the Maharajah to establish a base for expeditionary forces to subdue the local kingdoms, but he rebelled and established his own independent Rajahnate instead.

The arrival of Portuguese explorer Ferdinand Magellan in 1521 began a period of Spanish exploration and colonization.[11][12] Losing the favour of King Manuel I of Portugal for his plan of reaching the Spice Islands by sailing west from Europe, Magellan offered his services to king Charles I of Spain (Charles V, Holy Roman Emperor). On 20 September 1519, Magellan led five ships with a total complement of 250 people from the Spanish fort of Sanlúcar de Barrameda en route to southeast Asia via the Americas and Pacific Ocean. They reached the Philippines on 16 March 1521. Rajah Kolambu the king of Mazaua told them to sail for Cebu, where they could trade and obtain provisions. Arriving in Cebu City, Magellan, with Enrique of Malacca as translator, befriended Rajah Humabon the Rajah or King of Cebu, and persuaded the natives to ally themselves with Charles I of Spain. Humabon and his wife were given Christian names and baptized as Carlos and Juana. The Santo Niño was presented to the native queen of Cebu, as a symbol of peace and friendship between the Spaniards and the Cebuanos. On 14 April Magellan erected a large wooden cross on the shores of Cebu. Afterwards, about 700 islanders were baptized. Magellan soon heard of datu Lapu-Lapu, a native king in nearby Mactan Island, a rival of the Rajahs of Cebu. It was thought that Humabon and Lapu–Lapu had been fighting for control of the flourishing trade in the area. On 27 April the Battle of Mactan occurred, where the Spaniards were defeated and Magellan was killed by the natives of Mactanin Mactan Island. According to Italian historian and chronicler Antonio Pigafetta, Magellan's body was never recovered despite efforts to trade for it with spice and jewels. Magellan's second-in-command, Juan Sebastián Elcano, took his place as captain of the expedition and sailed the fleet back to Spain, circumnavigating the world.

Survivors of the Magellan expedition returned to Spain with tales of a savage island in the East Indies. Consequently, several Spanish expeditions were sent to the islands but all ended in failure. In 1564, Spanish explorers led by Miguel López de Legazpi, sailing from Mexico, arrived in 1565, and established a colony. The Spaniards fought the King, Rajah Tupas, and occupied his territories. The Spaniards established settlements, trade flourished and renamed the island to "Villa del Santísimo Nombre de Jesús" (Town of the Most Holy Name of Jesus). Cebu became the first European settlement established by the Spanish Cortés in the Philippines. In 1595, the Universidad de San Carlos was established and in 1860, Cebu opened its ports to foreign trade. The first printing house (Imprenta de Escondrillas y Cia) was established in 1873 and in 1880, the Colegio de la Inmaculada Concepcion (College of the Immaculate Conception) was established and the first periodical The Bulletin of Cebu ("El Boletin de Cebú") began publishing in 1886. In 1898, the island was ceded to the United States after the Spanish–American War and Philippine–American War. In 1901, Cebu was governed by the United States for a brief period, however it became a charter province on 24 February 1937 and was governed independently by Filipino politicians.

In February 2012 Cebu island experienced the effects of magnitude 6.7 earthquake on the neighboring island of Negros and was the largest quake in the area for 90 years. The tremor shook buildings but there were no reports of major building damage or loss of life on Cebu Island itself. This tremor was caused by a previously unrecorded fault. In October 2013, Cebu and Bohol were hit by record-setting 7.2 magnitude earthquake which left more than 100 dead, and collapsed some buildings, including 5 historical churches. There were over 700 aftershocks.