Background: Non-governmental organisations (NGOs) collect and generate vast amounts of potentially rich data, most of which are not used for research purposes. Secondary analysis of NGO data (their use and analysis in a study for which they were not originally collected) presents an important but largely unrealised opportunity to provide new research insights in critical areas, including the evaluation of health policy and programmes. Methods: A scoping review of the published literature was performed to identify the extent to which secondary analysis of NGO data has been used in health policy and systems research (HPSR). A tiered analytical approach provided a comprehensive overview and descriptive analyses of the studies that (1) used data produced or collected by or about NGOs; (2) performed secondary analysis of the NGO data (beyond the use of an NGO report as a supporting reference); and (3) analysed NGO-collected clinical data. Results: Of the 156 studies that performed secondary analysis of NGO-produced or collected data, 64% (n = 100) used NGO-produced reports (mostly to a limited extent, as a contextual reference or to critique NGO activities) and 8% (n = 13) analysed NGO-collected clinical data. Of these studies, 55% (n = 86) investigated service delivery research topics and 48% (n = 51) were undertaken in developing countries and 17% (n = 27) in both developing and developed countries. NGOs were authors or co-authors of 26% of the studies. NGO-collected clinical data enabled HPSR within marginalised groups (e.g. migrants, people in conflict-affected areas), albeit with some limitations such as inconsistent and missing data. Conclusion: We found evidence that NGO-collected and produced data are most commonly perceived as a source of supporting evidence for HPSR and not as primary source data. However, these data can facilitate research in under-researched marginalised groups and in contexts that are hard to reach by academics such as conflict-affected areas. NGO-academic collaboration could help address issues of NGO data quality to facilitate their more widespread use in research. The use of NGO data use could enable relevant and timely