We aimed to synthesise data on issues related to stakeholder perceptions of privacy, trust, and transparency in use of secondary data. A systematic literature review of healthcare consumer attitudes towards the secondary use and sharing of health administrative and clinical trial data was conducted. EMBASE/MEDLINE, Cochrane Library, PubMed, CINAHL, Informit Health Collection, PROSPERO Database of Systematic Reviews, PsycINFO, and ProQuest databases were searched. Eligible articles included those reporting qualitative or quantitative original research and published in English. No restrictions were placed on publication dates, study design or disease setting. One author screened articles for eligibility, and two authors were involved in the full text review process. Data was extracted using a pre-piloted data extraction template by one author and checked by another. Conflicts were resolved by consensus. Quality and bias were assessed using the QualSyst criteria for qualitative and quantitative studies. This paper focuses on a subset of 35 articles identified from the wider search which focus on issues of privacy, trust, and transparency. Studies included a total of 56,365 respondents. Results of this systematic literature review indicate that while respondents identified advantages in sharing health data, concerns relating to trust, transparency, and privacy remain. Organisations collecting health data and those who seek to share data or undertake secondary data analysis should continue to develop trust, transparency, and privacy with healthcare consumers through open dialogue and education. Consideration should be given to these issues at all stages of data collection including the conception, design, and implementation phases. While individuals understand the benefits of health data sharing for research purposes, ensuring a balance between public benefit and individual privacy is essential. Researchers and those undertaking secondary data analysis need to be cognisant of these key issues at all stages of their research. Systematic review registration: PROSPERO registration number CRD42018110559 (update June 2020).