Cities form the key context within which social, economic and environmental challenges for sustainable development will manifest in the years to come. As they face the grand societal challenges of climate change and the greening of energy systems, city governments are confronted with the challenge of designing and implementing workable policy strategies. We find that although much attention has been paid to low carbon energy transition in cities, there is surprisingly little attention to the dimension of governance, policy and politics in the scholarly literature. The main question in this guest editorial of the thematic issue, entitled ‘Governing the Climate Change Mitigation and Energy Transition Challenges in Cities’, is: How can effective policy strategies be designed and implemented to govern the challenges of climate change and energy transition in cities? We develop some preliminary answers to this question based on seven research papers that form the contribution to the thematic series. In particular, the various roles that cities play in governing the climate change challenges and energy transition require further description and analysis, specifying the different governing roles of urban actors and how the city—socially, institutionally or geophysically—forms the context within which governance initiatives and arrangements are formed and implemented, while cities themselves are in turn part of larger physical, infrastructural and institutional networks that influence and condition the local governance opportunities. A research agenda to explore the topic further must include particularly the following areas: the role of local government in the interplay between governance initiatives at multiple levels, the influence and the confluence of current (sectoral) policies, learning from a variation of practices of local low carbon policy, mapping the institutional dimension, mapping design and implementation practices of urban low carbon policy, assessing the effects and legitimacy of urban low carbon policies, further understanding of strategic action fields and lines of conflicts between (coalitions of) actors and identifying workable governance frameworks and policies supporting community-led energy initiatives.