Background: Health care delivery in schools is a frequently adopted approach to reduce health care inequalities. Lack of parental trust has been identified as impacting participation in school-based health care programs (SBHPs). The aim of our systematic review is to outline themes related to parental trust in SBHPs. Methods: We searched MEDLINE, Embase, CINHAL, ERIC, PsycInfo, and Web of Science for articles published between 1969 and 2019. Eligible studies: (1) were peer-reviewed primary research articles; (2) were school-based health interventions or screening programs; (3) included parental trust data; and (4) were carried out on schoolchildren from pre-K to grade 12. Study location, data collection date, number of participants, demographics, intervention type, study aim and methodology, and all trust themes mentioned, were extracted. Studies were critically appraised using the CASP checklist for qualitative research. Results: We identified 9 themes related to parental trust in SBHPs: (1) safety; (2) effectiveness; (3) health professionals' training and credentials; (4) communication; (5) confidentiality; (6) providers; (7) government, authorities, and health service; (8) the pharmaceutical industry; and (9) research and data sharing. Conclusions: The themes identified provide a framework for examining trust in SBHPs, and may guide the development of interventions to increase trust and engagement in SBHPs.