The EUAP maintains a central administration office at Hong Kong Baptist University, led by a Programme Coordinator. The secretariat is the first point of contact for all EUAP projects and cooperations.

The research section conducts research on EU economic and business issues, and organizes seminars / conferences on topics related to EU-HK business relations.

The EUAP is led by a Director-General and four Deputy Directors, two of whom are academic staff members of the Faculty of Social Sciences at Hong Kong Baptist University and one each from the Faculty of Arts at University of Hong Kong and the Faculty of Law at Chinese University of Hong Kong.

Steering Committee
The Steering Committee oversees the planning and implementation of EUAP activities. It consists of two representatives each of HKBU, HKU and CUHK plus one co-opted member from the HK civil service.

Advisory Committee
The Advisory Committee consists of representatives of civil society partners, media, business, law and the Office of the European Union to Hong Kong and Macao. Its members assist in activities and planning and provide feedback to the Steering Committee and the Executive.