The Portuguese built Fort Jesus in 1593. The site chosen was a coral ridge at the entrance to the harbor. The Fort was designed by an Italian Architect and Engineer, Joao, Batista Cairato.

The earliest known plan of the Fort is in a manuscript Atlas by Manuel Godinho de Heredia - dated 1610 which shows the original layout of the buildings inside the Fort.

 Fort Jesus was built to secure the safety of Portuguese living on the East Coast of Africa. It has had a long history of hostilities of the interested parties that used to live in Mombasa. Perhaps no Fort in Africa has experienced such turbulence as Fort Jesus. Omani Arabs attacked the Fort from 1696 to 1698. The state of the Fort can be understood from the plan of Rezende of 1636 and other plans by Don Alvaro? Marquis of Cienfuegas and Jose? Lopes de Sa - made during the brief reoccupation by the Portuguese in 1728 - 1729. In the Cienfuegas plan, the names of the bastions are changed.

Between 1837 and 1895, the Fort was used as barracks for the soldiers. When the British protectorate was proclaimed on the 1st of July 1895, the Fort was converted into a prison. The huts were removed and cells were built. On the 24th October 1958, Fort Jesus was declared a National Park in the custody of the Trustees of the Kenya National Parks. Excavation was carried out and the Fort became a Museum in 1962. The Fort is now an important historical landmark in the East African region.

The Fort Jesus museum was built with a grant from the Gulbenkian Foundation. The exhibits consist of finds from archaeological excavations at Fort Jesus, Gede, Manda, Ungwana and other sites. Other objects on display were donated by individuals notably Mrs. J.C. White, Mr. C.E. Whitton and Mrs. W.S. Marchant. The Fort has lived through the years of hostilities and a hush climate and is structurally well - maintained.