Participation is recognised as having a key role in health, for increasing the relevance and effectiveness of health interventions, for the health promoting benefits of community empowerment and as an ethical imperative. Participatory approaches to health research are also increasingly valued for bringing the insights of lived experience, and more relevant research and action. In this paper, we explore key remaining issues in participatory action research highlighted by scholars, practitioners and published literature, and highlight some useful conceptual resources which help to better understand them. We distinguish participatory action research as a paradigm involving those most affected throughout the research process, contrasting it with the more limited use of participatory tools and methods. We outline several aspects of participatory action research in health that would benefit from further theoretical and practical development, including: shifting power in the research process; the compatibility of participatory research with biomedical research; linking local inquiry and action to broader changes in policy and practice; and working with experiential knowledge in a rigorous research process. We highlight useful theory from a range of disciplines (including beyond the participatory research literature) that helps to understand some of the key processes and dynamics implicated in the issues highlighted and how this affects the outcomes achieved. We outline and share these conceptual/theoretical resources, identified as part of preparation for conducting a realist review on participatory action research in health, to contribute to ongoing reflection and development in the field.