EIPA is an independent institute, with a Board of Governors composed of representatives of EU Member States and the Institute's associated members. These representatives form a permanent link between EIPA and national public administrations, and also guarantee a strong institutional network at the highest level of public administration throughout Europe.
The The Board of Governors is chaired by Mr Guy Verhofstadt (BE), former Prime Minister of Belgium, MEP since 2009 (leading the Group of the Alliance of Liberals and Democrats for Europe, ALDE), and founder of the inter-parliamentarian federalist Spinelli Group.

The Director-General, Prof. Dr Marga Pröhl (DE), former Head of Division in the Department of Administrative Modernisation, Federal Ministry of the Interior, Germany, is responsible for the formulation and implementation of the Institute's policies, day-to-day management and the representation of EIPA.

At the headquarters' offices, located in Maastricht, the Netherlands, EIPA has three Units dealing respectively with:

The Institute has established two centres across Europe, each with specific competences: 

EIPA's representative office in Brussels serves as a meeting point in the heart of the European Union and close to the European Institutions.