This paper discusses challenges of capacity building in sustainable urban energy planning and development in Western Balkan Countries (WBC). It identifies needs in training of municipal staff and addresses obstacles for transferring sustainable energy education from EU universities to universities of WBC. The analysis of the ten training courses developed and piloted in collaboration with academic and non-academic stakeholders in Bosnia and Herzegovina, Montenegro and Serbia shows that while international cooperation has a good potential to improve quality of capacity building and to catalyse university-society collaboration in WBC, significant efforts on national and local (university) levels are needed to fully capitalise on these opportunities. In particular, it is necessary to enhance an interdisciplinary approach to education in sustainable energy, incorporating economic, social and institutional aspects of energy production and consumption together with the technical ones. On the national level, the lifelong learning system should get political and financial support in WBC to ensure efficiency and continuity of the training activities.