Citation: Hughes ZE and Walsh TR (2015) Computational chemistry for graphene-based energy applications: progress and challenges. Nanoscale. 7: 6883-6908. Research in graphene-based energy materials is a rapidly growing area. Many graphene-based energy applications involve interfacial processes. To enable advances in the design of these energy materials, such that their operation, economy, efficiency and durability is at least comparable with fossil-fuel based alternatives, connections between the molecular-scale structure and function of these interfaces are needed. While it is experimentally challenging to resolve this interfacial structure, molecular simulation and computational chemistry can help bridge these gaps. In this Review, we summarise recent progress in the application of computational chemistry to graphene-based materials for fuel cells, batteries and photovoltaics. We also outline both the bright prospects and emerging challenges these techniques face for application to graphene-based energy materials in future.