INTRODUCTION: Mechanisms explain how implementation strategies work. Implementation research requires careful operationalisation and empirical study of the causal pathway(s) by which strategies effect change, and factors that may amplify or weaken their effects. Understanding mechanisms is critically important to replicate findings, learn from negative studies or adapt an implementation strategy developed in one setting to another. Without understanding implementation mechanisms, it is difficult to design strategies to produce expected effects across contexts, which may have disproportionate effects on settings in which priority populations receive care. This manuscript outlines the protocol for an Agency for Healthcare Research and Quality-funded initiative to: (1) establish priorities for an agenda to guide research on implementation mechanisms in health and public health, and (2) disseminate the agenda to research, policy and practice audiences. METHODS AND ANALYSIS: A network of scientific experts will convene in Deep Dive meetings across 3 years. A research agenda will be generated through analysis and synthesis of information from six sources: (1) systematic reviews, (2) network members approaches to studying mechanisms, (3) new proposals presented in implementation proposal feedback sessions, (4) working group sessions conducted in a leading implementation research training institute, (5) breakout sessions at the Society for Implementation Research Collaborations (SIRC) 2019 conference and (6) SIRC conference abstracts. Two members will extract mechanism-relevant text segments from each data source and a third member will generate statements as an input for concept mapping. Concept mapping will generate unique clusters of challenges, and the network will engage in a nominal group process to identify priorities for the research agenda. ETHICS AND DISSEMINATION: This initiative will yield an actionable research agenda to guide research to identify and test mechanisms of change for implementation strategies. The agenda will be disseminated via multiple channels to solicit feedback and promote rigorous research on implementation mechanisms.