City-level decision-making requires timely access to a wide range of relevant and comprehensible data and information. Although a wide range of research on energy and cities is on-going across the social, engineering and natural sciences, it cannot be taken for granted that the questions being asked and the way questions are structured reflect practitioner perspectives and requirements. This paper discusses the ways in which research questions are formed and interpreted by actors in academic research and research user communities. We also report a set of research questions produced via an initial trial of a two stage, participative process consisting of (a) a survey targeted at city-focussed practitioners in the United Kingdom (UK) with an interest in lower carbon energy futures; and (b) a workshop integrating practitioner and academic perspectives. Comparing the set of research questions identified with themes in the academic literature, we find that research and practitioner communities concur on the importance of reducing energy demand and also on a number of cross-cutting issues. However, we also find that academic research places a greater emphasis on the interfaces between the energy system and other urban systems. We conclude that the two stage, participative process followed can serve to generate and legitimate city-related research questions through collaboration between stakeholders and academic researchers.