Before the arrival of the Spaniards in the 16th century, Cebu then known as Zubu (or Sugbo) was an island inhabited by pagan, and islamic people who traded with other Asian civilizations.

Magellan Expedition

Losing favor for his plan of reaching the Spice Islands by sailing westward from King Manuel I of Portugal, Portuguese explorer Ferdinand Magellan offered his services to the Holy Roman Emperor, Charles V of Spain. On September 20, 1519, Magellan led five ships with a crew of 250 people out of the Spanish fort of San Lucar de Barrameda enroute to the Spice Islands via the Americas, and Pacific Ocean.

They reached the Philippine Islands on March 16, 1521. Rajah Kolambu the chieftain of Mazaua told them to sail for Cebu, where they could trade, and have provisions.

Arriving in Cebu City, Magellan, with Enrique of Malacca as translator, befriended Rajah Humabon the native chieftain of Cebu, and persuaded the natives of allegiance to Emperor Charles V of Spain. Rajah Humabon, and his wife were baptized as King Carlos, and Queen 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 April 14, Magellan erected a large wooden cross on the shores of Cebu. Afterwards, about 700 native Cebuanos were baptized.

Magellan soon heard of a tribal ruler named, Rajah Lapu-Lapu, in nearby Mactan Island. It was thought that Rajah Humabon, and Rajah Lapu-Lapu have been fighting for control of the flourishing trade in the area.

On April 27, the historic Battle of Mactan occurred where the Spaniards were defeated, and Magellan killed by native warriors. According to 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, and sailed the remainder of the fleet back to Spain, circumnavigating the world.

Spanish conquest and colonial period

 Survivors of the Magellan expedition brought tales of a savage island in the East Indies with them when they returned to Spain. Consequently, several follow-up expeditions were sent but all ended in failure.

Forty-four years after Magellan first set foot in Cebu; Spanish conquistadors led by Miguel López de Legazpi sailing from the western coast of Barra de Navidad, Jalisco, Mexico arrived in 1565, and established a colony. The Spaniards marched through the island, bombarded the palisades of chieftain Rajah Tupas, and destroyed the native villages. The Spaniards established settlements, trade flourished, and renamed the island to "Villa del Santíssimo Nombre de Jesús" (Town of the Most Holy Name of Jesus). Cebu became the first European settlement established by the Spanish Cortés in the Philippine Islands.

In 1860, Cebu opened its forts to foreign trade. The first printing house ("Imprenta de Escondrillas y Cia") was established in 1873. In 1880, Colegio de la Inmaculada Concepcion was established. The first periodical The Bulletin of Cebu ("El Boletin de Cebú") began publishing in 1886.

On June 12, 1898 marked the end of the Spanish period. In 1901, Cebu became a municipality, and on February 24, 1937, the island became a chartered province during the American period.

 World War II

Cebu, being the most densely populated island in the Philippines, served as a Japanese base during the Japanese occupation in World War II which began with the landing of Japanese soldiers in April 1942. Almost three years later in March 1945, combined Filipino and American forces landed and reoccupied the island during the liberation of the Philippines.

Cebuano rebel soldiers led by an American, James Cushing, is credited for the capture of the Koga Papers which is said to have changed the American plans to retake the Philippine Islands from Japanese occupation in 1944, by helping the United States and the Philippine Commonwealth troops enter Cebu in 1945.