Background Secondary use of health data provides opportunities to drive improvements in healthcare provision, personalised medicine, comparative effectiveness research, health services innovation, and policy and practice. However, secondary data use requires compliance with relevant legislation, implementation of technical safeguards, ethical data management, and respect for data sharers. Existing evidence suggests widespread support for secondary use of health data among the public, which co-exists with concerns about privacy, confidentiality and misuse of data. Balancing the protection of individuals' rights against the use of their health data for societal benefits is of vital importance, and trust underpins this process. The study protocol explores how to build public trust and confidence in the secondary use of health data through all key stakeholder groups in Ireland, towards developing a culture that promotes a safe and trustworthy use of data. Methods This study will adopt a qualitative cross-sectional approach conducted in accordance with the Consolidated Criteria for Reporting Qualitative Research COREQ guidelines. Participants in the study will include academics and researchers; healthcare professionals, data protection, ethics and privacy experts and data controllers; pharmaceutical industry and patients and public. Purposive and convenience sampling techniques will be utilised to recruit the participants, and data will be collected utilizing focus groups that may be supplemented with semi-structured interviews. Data will be coded by themes using reflexive thematic analysis (TA) and collective intelligence (CI) will be convened post-analysis to explore the preliminary findings with the participants. Ethics and Dissemination Ethical approval was obtained from the Royal College of Surgeons in Ireland Research Ethics Committee (REC202208013). Final data analysis and dissemination is expected by Q1 2024. Findings will be disseminated through peer-reviewed journal publications, presentations at relevant conferences, and other academic, public and policy channels. Lay summaries will be designed for Public and Patient Involvement (PPI) contributors and general public.