The French Research Centre in Jerusalem is a research unit under the supervision of the French Ministry of Europe and Foreign Affairs (MEAE), and of the National Centre for Scientific Research (CNRS). It belongs to the network of French Research Institutes based abroad (UMIFRE n° 7 CNRS – MEAE) headed by the Directorate-General of Global Affairs, Culture, Teaching and International Development and Partnerships (DGM) of the MEAE. It is also a Service and Research Unit of the CNRS (USR 3132).

The functioning of the CRFJ is defined in an inter-ministerial agreement signed on 5 December 2000 and regularly updated. This agreement provides that all scientific activities of the CRFJ follows the missions of the research units associated to CNRS.

In application of the above, the CRFJ Director is appointed by the MEAE. He is also the Director of the CNRS Research Unit, USR 3132.

In the CNRS, the CRFJ is headed by the French National Institute of Social Sciences and Humanities (INSHS).