In accordance with the Statute of the Jagiellonian College, currently all the significant powers concerning the functioning of the School are held by the Board of Trustees. It is the Board that has the right to appoint and dismiss the rector, the deputy rectors and chancellor, makes all the most important decisions concerning the finances of the College. It is also the prerogative of the Board of Trustees to make changes in the Statute of the College.

The five-member Board, appointed at the beginning of 2013, is currently chaired by Jakub Piechota Ph.D.