Health system resilience reflects the ability to continue service delivery in the face of extraordinary shocks. We examined the case of the United Nations Relief and Works Agency (UNRWA) and its delivery of services to Palestine refugees in Syria during the ongoing crisis to identify factors enabling system resilience. The study is a retrospective qualitative case study utilizing diverse methods. We conducted 35 semi-structured interviews with UNRWA clinical and administrative professionals engaged in health service delivery over the period of the Syria conflict. Through a group model building session with a sub-group of eight of these participants, we then elicited a causal loop diagram of health system functioning over the course of the war, identifying pathways of threat and mitigating resilience strategies. We triangulated analysis with data from UNRWA annual reports and routine health management information. The UNRWA health system generally sustained service provision despite individual, community and system challenges that arose during the conflict. We distinguish absorptive, adaptive and transformative capacities of the system facilitating this resilience. Absorptive capacities enabled immediate crisis response, drawing on available human and organizational resources. Adaptive capacities sustained service delivery through revised logistical arrangements, enhanced collaborative mechanisms and organizational flexibility. Transformative capacity was evidenced by the creation of new services in response to changing community needs. Analysis suggests factors such as staff commitment, organizational flexibility and availability of collaboration mechanisms were important assets in maintaining service continuity and quality. This evidence regarding alternative strategies adopted to sustain service delivery in Syria is of clear relevance to other actors seeking organizational resilience in crisis contexts.