Palestinian refugees served by the United Nation Relief and Works Agency for Palestine Refugees in the Near East (UNRWA) are experiencing increasing rates of diagnosis of non-communicable diseases. In response, in 2011 UNRWA initiated an Agency-wide programme of primary healthcare reform, informed by the Chronic Care Model framework. Health services were reorganized following a family-centred approach, with delivery by multidisciplinary family health teams supported by updated technical advice. An inclusive clinical information system, termed e-Health, was implemented to collect a wide range of health information, with a focus on continuity of treatment. UNRWA was able to bring about these wide-ranging changes within its existing resources, reallocating finances, reforming its payment mechanisms, and modernizing its drug-procurement policies. While specific components of UNRWA’s primary healthcare reform are showing promising results, additional efforts are needed to empower patients further and to strengthen involvement of the community.