The President is chair of the Board of Trustees and is nominated by the Members of the Board of Trustees on consideration of proposals by the Assembly of Directors and appointed by the Federal Ministry for Education and Research (BMBF) for a tenure of four years. 

The President is the external representative of the Foundation. In particular the incumbent represents the common interests of the institutes vis-à-vis funding bodies, politics, the public and academic organisations as well as collaborating in national and international academic bodies and organisations. In employment law terms the President is the supervisor of the Directors of the Institutes and the Executive Director.

Following the early foundation years in which two chairs of the Board of Trustees were deployed by the BMBF (MinDir Karsten Brenner and MDir Dr. Uwe Bake), the Cologne-based historian Professor Dr. Dr. h. c. Wolfgang Schieder was nominated by the Board of Trustees on 10 February 2003 for a first tenure and again on 20 November 2006 for a sec On 1 May 2009  the Director of the Institute for European History in Mainz, Professor Dr. Dr. h. c. Heinz Duchhardt took up office as President. From 1 March 2015 to 28 February 2023, the Munich sinologist Prof. Dr. Hans van Ess was President of the Max Weber Foundation. Since 1 March 2023, the Berlin historian Prof. Dr. Dr. h.c.. Ute Frevert heads the foundation.