Background The need for better methods for evaluation in health research has been widely recognised. The ‘complexity turn’ has drawn attention to the limitations of relying on causal inference from randomised controlled trials alone for understanding whether, and under which conditions, interventions in complex systems improve health services or the public health, and what mechanisms might link interventions and outcomes. We argue that case study research—currently denigrated as poor evidence—is an under-utilised resource for not only providing evidence about context and transferability, but also for helping strengthen causal inferences when pathways between intervention and effects are likely to be non-linear. Main body Case study research, as an overall approach, is based on in-depth explorations of complex phenomena in their natural, or real-life, settings. Empirical case studies typically enable dynamic understanding of complex challenges and provide evidence about causal mechanisms and the necessary and sufficient conditions (contexts) for intervention implementation and effects. This is essential evidence not just for researchers concerned about internal and external validity, but also research users in policy and practice who need to know what the likely effects of complex programmes or interventions will be in their settings. The health sciences have much to learn from scholarship on case study methodology in the social sciences. However, there are multiple challenges in fully exploiting the potential learning from case study research. First are misconceptions that case study research can only provide exploratory or descriptive evidence. Second, there is little consensus about what a case study is, and considerable diversity in how empirical case studies are conducted and reported. Finally, as case study researchers typically (and appropriately) focus on thick description (that captures contextual detail), it can be challenging to identify the key messages related to intervention evaluation from case study reports. Conclusion Whilst the diversity of published case studies in health services and public health research is rich and productive, we recommend further clarity and specific methodological guidance for those reporting case study research for evaluation audiences.