Abstract Background Over the past four decades, drought episodes in the Eastern Mediterranean Region (EMR) of the of the World Health Organization (WHO) have gradually become more widespread, prolonged and frequent. We aimed to map hotspot countries and identified key strategic actions for health consequences. Methods We reviewed scientific literature and WHO EMR documentation on trends and patterns of the drought health consequences from 1990 through 2019. Extensive communication was also carried out with EMR WHO country offices to retrieve information on ongoing initiatives to face health consequences due to drought. An index score was developed to categorize countries according vulnerability factors towards drought. Results A series of complex health consequences are due to drought in EMR, including malnutrition, vector-borne diseases, and water-borne diseases. The index score indicated how Afghanistan, Yemen and Somalia are “hotspots” due to poor population health status and access to basic sanitation as well as other elements such as food insecurity, displacement and conflicts/political instability. WHO country offices effort is towards enhancing access to water and sanitation and essential healthcare services including immunization and psychological support, strengthening disease surveillance and response, and risk communication. Conclusions Drought-related health effects in the WHO EMR represent a public health emergency. Strengthening mitigation activities and additional tailored efforts are urgently needed to overcome context-specific gaps and weaknesses, with specific focus on financing, accountability and enhanced data availability.