Membership of the PERC is based on affiliation to the ITUC. It consists of 90 national centres affiliated to the ITUC. The PERC is also open to Global Union Federations at the international level and to European Industry Federations at the European level. The institutions of the PERC are the General Assembly, the Executive Committee, the Steering Committee and the Secretariat.

The General Assembly meets at least once every 4 years to determine priorities for action in the region, receive reports on activities, consider any rule changes, approve the membership of the Executive Committee, and elect the PERC President, General Secretary and Vice-Presidents.

The 5th PERC General Assembly in December 2023 elected Igor Zubcu, leader of the the National Confederation of Trade Unions of Moldova (CNSM), as the President of PERC. It elected Vice-Presidents to form a balanced and committed leadership team to guide the PERC programme implementation and to support the President and the Secretariat. The current Vice-Presidents are: Ms Arzu Cerkezoglu (DISK President),
Mr Satybaldy Dauletalin (FPRK President), Ms Irina Gorshkova (KTR Secretary on Gender), Ms Raisa Liparteliani (GTUC Vice-President), Ms Julie Lodrup (LO-Norway 1st Secretary), Mr Sattar Mehbaliyev (AHIK President), Mr Piotr Ostrowski (OPZZ President), Mr Marcus Strohmeier (OGB Head of International Department)
Ms Anisa Subashi (KSSH Vice President) and then (rotation agreement) Ms Arjola Alika (BSPSH International Relations), Mr Mikhaylo Volynets (KVPU President)

ETUC General Secretary Esther Lynch is the General Secretary of PERC.

The Executive Committee meets at least once a year to receive reports on activities, identify priorities and define action plans. Where necessary it can set up networks, programmes, task forces for addressing specific issues and committees, as well as receiving the accounts and preparing the meetings of the General Assembly.

The PERC Steering Committee is composed of the General Secretary, President, Vice-Presidents, Executive Secretary, and presidents of Women’s and Youth Committees shall meet at least twice a year to assure the continuity of the PERC operation, treat matters of urgency as mandated by the Executive Committee and to prepare meetings of the Executive Committee.

The Secretariat is composed of the PERC General Secretary and officers designated by him or her and by the General Secretary of the ITUC. An Executive Secretary is appointed by the ITUC and ETUC General Secretaries acting in concert. The Executive Secretary is Anton Leppik.

The PERC sets up different task forces to fulfill its objectives and works with various sub-regional and transnational trade union forums and networks, such as the South-East European Trade Union Forum and the Baltic Sea Trade Union Network.