The Directorate (DIR) is the governing body responsible for the management of the Core Project and the Flagship as a whole. It manages the Project and its finances, ensures that it fulfils its contractual obligations, and links the Science and Infrastructure Board and the Stakeholder Board.

The Coordinator (EPFL) named Philippe Gillet as the Director General of the Human Brain Project, as of 1st April 2016. The Directorate has the following members: