Introduction <p>Malaria is a vector-borne disease that poses crucial health challenges in Iran. The malaria outbreak in southeastern Iran over the two years preceding 2023 supports the hypothesis that climate change is linked to increased malaria cases. This study investigated the effect of climate change on malaria incidence in five counties under the jurisdiction of Zahedan University of Medical Sciences (ZUMS).</p> Methods <p>This cross-sectional study utilized malaria incidence data from the Health Deputy of ZUMS and climatic variables from the Meteorological Organization, covering the period from 2017 to 2023. The effects of climatic factors on malaria occurrence were analyzed using SPSS 25.</p> Results <p>Over the past five years, the average annual temperature in the five cities has increased by approximately 3 °C, while average humidity has decreased by about 2%. The proportion of imported malaria cases decreased from approximately 74% in 2017 to about 41% in 2023. Cases of falciparum and mixed infections in 2023 have increased nearly threefold compared to 2017.</p> Conclusion <p>Climate parameters that influence malaria incidence must be integrated into malaria control and prevention planning to mitigate both human and financial costs. Weather monitoring and early warning systems can reduce risk by identifying precursors to epidemics of vector-borne diseases.</p>