A significant fraction of Brazil's population has been exposed to drought in recent years, a situation that is expected to worsen in frequency and intensity due to climate change. This constitutes a current key environmental health concern, especially in densely urban areas such as several big cities and suburbs. For the first time, a comprehensive assessment of the short‐term drought effects on weekly non‐external, circulatory, and respiratory mortality was conducted in 13 major Brazilian macro‐urban areas across 2000–2019. We applied quasi‐Poisson regression models adjusted by temperature to explore the association between drought (defined by the Standardized Precipitation‐Evapotranspiration Index) and the different mortality causes by location, sex, and age groups. We next conducted multivariate meta‐analytical models separated by cause and population groups to pool individual estimates. Impact measures were expressed as the attributable fractions among the exposed population, from the relative risks (RRs). Overall, a positive association between drought exposure and mortality was evidenced in the total population, with RRs varying from 1.003 [95% CI: 0.999–1.007] to 1.010 [0.996–1.025] for non‐external mortality related to moderate and extreme drought conditions, from 1.002 [0.997–1.007] to 1.008 [0.991–1.026] for circulatory mortality, and from 1.004 [0.995–1.013] to 1.013 [0.983–1.044] for respiratory mortality. Females, children, and the elderly population were the most affected groups, for whom a robust positive association was found. The study also revealed high heterogeneity between locations. We suggest that policies and action plans should pay special attention to vulnerable populations to promote efficient measures to reduce vulnerability and risks associated with droughts.