The fort is triangular in shape, with two facing the sea sides and the third facing the land side. The two facing the sea sides were defended with artillery and the third was fortified with a wooden palisade..

The date of construction of the stone fort is uncertain, although there are claims that an Antonio Campioni built it in 1630, and the gate of the fort bears the date 1738 alongside the arms of Castile and Leon. It is certain, however, that the fort underwent renovations in the later 19th century as part of a larger building program to improve Cebu.

Fort San Pedro became a part of the American Warwick barracks during the American regime. This occurred during 1937 to 1941, when the barracks was converted into a school where many Cebuanos received their formal education. During World War II, from 1942 to 1945, Japanese residents of the city took refuge within its walls. When the battle to liberate Cebu from the Imperial Japanese forces was fought, Fort San Pedro served as an emergency hospital for the wounded.