Abstract Background There is a growing concern that the quality of health systems in humanitarian crises and the care they provide has received little attention. To help better understand current practice and research on health system quality, this paper aimed to examine the evidence on the quality of health systems in humanitarian settings. Methods This systematic review was based on the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) protocol. The context of interest was populations affected by humanitarian crisis in low- and middle- income countries (LMICs). We included studies where the intervention of interest, health services for populations affected by crisis, was provided by the formal health system. Our outcome of interest was the quality of the health system. We included primary research studies, from a combination of information sources, published in English between January 2000 and January 2019 using quantitative and qualitative methods. We used the High Quality Health Systems Framework to analyze the included studies by quality domain and sub-domain. Results We identified 2285 articles through our search, of which 163 were eligible for full-text review, and 55 articles were eligible for inclusion in our systematic review. Poor diagnosis, inadequate patient referrals, and inappropriate treatment of illness were commonly cited barriers to quality care. There was a strong focus placed on the foundations of a health system with emphasis on the workforce and tools, but a limited focus on the health impacts of health systems. The review also suggests some barriers to high quality health systems that are specific to humanitarian settings such as language barriers for refugees in their host country, discontinued care for migrant populations with chronic conditions, and fears around provider safety. Conclusion The review highlights a large gap in the measurement of quality both at the point of care and at the health system level. There is a need for further work particularly on health system measurement strategies, accountability mechanisms, and patient-centered approaches in humanitarian settings.