BACKGROUND: Closing the gap between research production and research use is a key challenge for the health research system. Stakeholder engagement is being increasingly promoted across the board by health research funding organisations, and indeed by many researchers themselves, as an important pathway to achieving impact. This opinion piece draws on a study of stakeholder engagement in research and a systematic literature search conducted as part of the study. MAIN BODY: This paper provides a short conceptualisation of stakeholder engagement, followed by 'design principles' that we put forward based on a combination of existing literature and new empirical insights from our recently completed longitudinal study of stakeholder engagement. The design principles for stakeholder engagement are organised into three groups, namely organisational, values and practices. The organisational principles are to clarify the objectives of stakeholder engagement; embed stakeholder engagement in a framework or model of research use; identify the necessary resources for stakeholder engagement; put in place plans for organisational learning and rewarding of effective stakeholder engagement; and to recognise that some stakeholders have the potential to play a key role. The principles relating to values are to foster shared commitment to the values and objectives of stakeholder engagement in the project team; share understanding that stakeholder engagement is often about more than individuals; encourage individual stakeholders and their organisations to value engagement; recognise potential tension between productivity and inclusion; and to generate a shared commitment to sustained and continuous stakeholder engagement. Finally, in terms of practices, the principles suggest that it is important to plan stakeholder engagement activity as part of the research programme of work; build flexibility within the research process to accommodate engagement and the outcomes of engagement; consider how input from stakeholders can be gathered systematically to meet objectives; consider how input from stakeholders can be collated, analysed and used; and to recognise that identification and involvement of stakeholders is an iterative and ongoing process. CONCLUSION: It is anticipated that the principles will be useful in planning stakeholder engagement activity within research programmes and in monitoring and evaluating stakeholder engagement. A next step will be to address the remaining gap in the stakeholder engagement literature concerned with how we assess the impact of stakeholder engagement on research use.