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, 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 and Vice-Presidents.

The PERC President is elected for a 4-year term. The Third General Assembly in December 2015 elected Irakli Petriashvili, President of the GTUC-Georgia, as PERC President, and eight Vice-Presidents: Ana Maria Corral, UGT, Spain, Erich Foglar, OeGB, Austria, Marija Hanzevacki, NHS, Croatia, Nataliya Levitska, KVPU, Ukraine, Sattar Mehbaliyev, AHIK, Azerbaijan, Ellen Nygren, LO, Sweden, Mikhail Shmakov, FNPR, Russia, and Anna Wolanska, NSZZ Solidarnosc, Poland..

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 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.

According to PERC constitution the ETUC General Secretary is also General Secretary of the PERC. The PERC General Secretary is Luca Visentini, 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.