Refugee settlements are frequently located in isolated and remote areas, characterized by poor-quality land and harsh climatic conditions. Zaatari camp in Jordan has suffered and continues to suffer from rainwater floods every winter. This study uses GIS analysis to assess flood risk in the camp, revealing that 61.1% of the area is moderately risky, while 0.84% and 22.42% are very high and high-risk zones respectively. The highest risk areas are near the camp boundary. This study recommends a structural intervention and first-class priority at the entrance area of the camp as it is located within a high-risk area and is of vital importance from a functional standpoint. These recommendations range to areas within high-risk zone in (1, 2, 7, 12) districts, to moderate risk zone in (4,8,11) districts with precautionary and preventive measures. In addition, some structural solutions can be implemented in several stages. This research is significant not only for managing flood risk in Zaatari but also for providing a replicable methodology for similar humanitarian settlements worldwide.