ACER's headquarters are located in Ljubljana, Slovenia, and has about 170 employees, both permanent staff and experts seconded by national regulatory authorities.

The battle for the agency's headquarters was long and tense. Ljubljana prevailed over Bratislava and Bucharest.

Distinct from the EU institutions, agencies are set up as separate legal entities to perform specific technical and scientific tasks that help EU institutions and Member States to implement policies and take decisions. ACER is an independent body to foster the integration and completion of the Eu​​ropean Internal Energy Market for electricity and natural gas​. By fostering cooperation among National Regulatory Authorities, ACER ensures that the integration of national energy markets and the implementation of legislation in the Member States are met according to the EU's energy policy objectives and regulatory frameworks.

The overall purpose of ACER is achieving a transition of the European energy system in line with the political objectives set, reaping benefits of increased energy market integration across Europe, and securing low-carbon supply at least possible cost for European businesses and citizens.