The main funding for the Berenike Project is provided by the Netherlands Foundation for Scientific Research, Humanities Department (GW-NWO), which has funded the project from 1995 to 1999 and again during the period 2000-2003, The National Geographic Society, which has funded the project from 1994 to 2000, the Samuel H. Kress Foundation and the University of Delaware.

Many other organization, companies and private donors sponsor specific projects related to the work at Berenike. Among these are the Netherlands Ministry of Foreign Affairs, the Dorot Foundation, the Columbia University New York, the Gratama Foundation, the Utopa Foundation, the Leiden University Alumni Fund, 3 Com Computer Co-operation, Leiden University (section Egyptology), Philips Egypt, Organon, the American Philosophical Society, Dionysos Systems and the National Endowment for the Humanities.