The fortress was built circa 300 AD by Emperor Diocletian in order to protect the entrance to an ancient canal, previously rebuilt by Trajan, that linked the Nile with the Red Sea.

[citation needed] Some historical sources, such as John of Nikiu, report that a fortress named Babylon was first founded by Nebuchadnezzar II circa 568 BC, at the site where an ancient Egyptian canal linked the Nile with the Red Sea.

[7] The construction of the present Babylon Fortress (whose remains are visible today) has been attributed by more recent archeological research to the reign of Diocletian (r. 285–305), who expanded the fortifications at the mouth of the canal around 300 AD.

[10][11] The large new fortress, probably made necessary after the Crisis of the Third Century, provided a considerable defense for both the land and sea routes in the region.

The history of this conquest, and of the subsequent rule of the then still Coptic Christian city by the Arabs, is told by John Bishop of Nikiû in his Chronicle, which survives now only in Ethiopic manuscripts.