The effect of social, political, and economic context on treatment seeking and the effective case management of malaria is widely recognised. In refugee settings, the whole balance of society has been upset and both intra and inter- household relationships have been extensively disrupted. Many refugees undergo trauma, which may affect their perceptions of health and ill health. This study, investigated the factors influencing effective case management of malaria in the Kakuma refugee camp using a variety of data collection methods including: indepth interviews, focus group discussions, observations of clinical management and a parasite prevalence survey. The refugees and the providers of health care in Kakuma perceived that the burden of malaria was high, but the parasitological data were of insufficient quality to confirm these perceptions. Clinical management and parasitological diagnosis of malaria were insufficient and affected by: inadequately qualified and poorly motivated staff, budgetary, logistical and security constraints. Awareness of the symptoms of malaria among the refugees were relatively high, but treatment seeking was affected by the insufficient quality of malaria management, the context of the refugee camp setting, and the experiences suffered in becoming a refugee. In particular, the loss of a sense of agency and the on-going problems of nutritional and physical security influenced the refugees' motivation to seek treatment. The establishment of community health committees could provide a mechanism to address some of these contextual issues by: strengthening the relationships among the refugees health care providers and camp management; providing the refugees with a greater sense of agency; helping in the support and motivation of the health staff and providing a forum for the development of appropriate disease management programmes. This study underlines that understanding the setting and circumstances of becoming and remaining a refugee is essential to developing effective disease management strategies for refugees.