Introduction Identifying research gaps can inform the design and conduct of health research, practice and policies by informing the current body of evidence. Audiences including researchers, clinical guideline developers, clinicians, policymakers, research regulatory bodies, funders and patients/the public can also benefit from understanding the status of research and research gaps to make informed choices. This study aims to explore how key informants define research gaps and characterise methods/practices used to identify and display gaps in health research to inform future research practice and policies.Methods and analysis This is an exploratory qualitative study using semi-structured in-depth interviews. The participants will be recruited by purposive sampling from initiatives and organisations previously identified in a scoping review on methods to identify, prioritise and display gaps in health research. We anticipate performing up to 28 interviews with the different key informant groups who are involved in using evidence to inform health policy, practice and research. Interviews will be thematically analysed as outlined by Braun and Clarke. The qualitative data-analysis software NVivo V.12 Pro will be used to aid data management and analysis.Discussion This is the protocol for a follow-up study that aims to complement and enrich the findings of the scoping review on methods to identify, prioritise and display gaps in health research. The overall project aims to develop methodological guidance for describing, identifying and displaying gaps in health research.Ethics and dissemination The research obtained ethical approval from the University of Liverpool, UK. The findings will be disseminated via conferences, meetings (organised by the Methods in Research on Research project), peer-reviewed publications and lay magazines because the study participants will include the public/patients.