This study of the United Nations Relief and Works Agency for Palestinian Refugees in the Near East (UNWRA) in Lebanon and Jordan explored their degree of health system resilience to the impact of shocks and stressors arising from the Syrian crisis. The study used a capacity-oriented resilience framework (including absorption, adaptation and transformation) with professionals at primary care, area and country management levels; 62 semi-structured interviews were done (30 in Lebanon in November–December 2016, and 32 in Jordan in January 2017). Participants reflected on changes in population health status and health service delivery during the Syrian crisis, notably with respect to the influx of refugees from Syria. Interviews were analysed through inductive thematic analysis and used to critically interrogate health systems resilience against a pro-capacities framework. We find that UNRWA systems in Lebanon and Jordan were broadly resilient, deploying diverse strategies to address health challenges and friction between host and refugee populations. Absorptive capacity was evidenced by successful accommodation of increased patient numbers across most service areas. Adaptive capacities were reflected in broadening of collaboration and reconfiguration of staff roles to enhance service delivery. Transformative capacities were demonstrated in the revision of the service packages provided. While manifest as technical capacities, these clearly drew upon solidarity and commitment linked to the political context of the Palestinian experience. The study adds to the limited literature on health system and organizational resilience and indicates that capacity-oriented framings of resilience are valuable in extracting generalizable lessons for health systems facing adversity. The proposed resilience framework promises to guide strategies for sustained care delivery in these contexts.