Khafajah was occupied during the Early Dynastic Period, through the Sargonid Period, then came under the control of Eshnunna after the fall of the Ur III Empire. Later, after Eshnunna was captured by Babylon, a fort was built at the site by Samsu-iluna of the First Babylonian Dynasty and named Dur-Samsuiluna.

The history of Khafajah is known in somewhat more detail for a period of several decades as a result of the discovery of 112 tablets in a temple of the god Sin. The tablets constitute part of an official archive and include mostly loan and legal documents.