ABSTRACT Background We analysed the spatial and spatiotemporal patterns of visceral leishmaniasis (VL) mortality at the municipality level in an endemic state in the southern Amazon region of Brazil. Individual-level factors associated with death due to VL were also investigated. Methods All VL cases and deaths reported between 2007 and 2018 were included. The global and local bivariate Moran's index assessed the space–time autocorrelation of smoothed triennial VL mortality. Kulldorff's scan statistics investigated spatial and spatiotemporal clusters. A multivariable logistic regression explored sociodemographic, diagnostic and clinical variables associated with death due to VL. Results We observed an overall VL mortality and lethality of 0.14 cases/100 000 inhabitants and 11.2%, respectively. A total of 14% of the municipalities registered at least one VL-related death. In the southeastern mesoregion of the state, we detected high-risk spatial (relative risk [RR] 14.14; p<0.001) and spatiotemporal (RR 15.91; p<0.001) clusters for VL mortality. Bivariate Moran's analysis suggested a high space–time autocorrelation of VL mortality. Death by VL was associated with age ≥48 y (odds ratio [OR] 7.2 [95% confidence interval {CI} 3.4 to 15.3]), displacement for notification (OR 3.3 [95% CI 1.5 to 7.2]) and occurrence of oedema (OR 2.8 [95% CI 1.3 to 6.1]) and bleeding (OR 5.8 [95% CI 2.6 to 12.8]). Conclusions VL mortality has a heterogeneous spatiotemporal distribution. The death-related factors suggest late diagnosis as an underlying cause of mortality.