Background <p>In Zanzibar, malaria epidemiology has changed within the past 10&#xa0;years, from focal, near-elimination transmission to recurrent and more widespread outbreaks. The observed changes culminated in a large-scale epidemic between November 2023 and March 2024 including 23,569 confirmed malaria cases.</p> Methods <p>This study investigated the epidemiological characteristics of the 21-week outbreak by characterizing the risk profile of affected individuals, identifying malaria hotspots across space and time, and determining the association between malaria incidence and precipitation and temperature.</p> Results <p>Males, individuals aged 15–35, urban residents, and those reporting to not sleep under insecticide-treated nets had a higher malaria risk. One significant space–time cluster was identified in the urban southwest of Unguja. The weekly number of malaria cases was significantly associated with the average weekly temperature, with an 8-week lag time.</p> Conclusions <p>The results indicate a serious setback in the pursuit of malaria elimination in Zanzibar and call for intensified malaria interventions targeting high-risk populations.</p>