Objective To analyse the spatial, temporal and spatial–temporal patterns of infant mortality associated with congenital toxoplasmosis in Brazil between the years 2000 and 2020. Methods Ecological study of time series, with spatial analysis and spatiotemporal scan of infant mortality associated with congenital toxoplasmosis from the records of deaths of the Mortality Information System of the Brazilian Ministry of Health. The rates were smoothed by the Local Empirical Bayesian model. The Global Moran Index, Global Geary's Contiguity and Getis‐Ord General statistics were calculated for spatial autocorrelation assessment. The trends were evaluated by the Joinpoint method. Results We identified 1183 infant deaths associated with congenital toxoplasmosis in Brazil between 2000 and 2020. The predominant characteristics were male sex (52.1%), post‐neonatal age group (51.9%), white race/colour (45.7%), and Southeast region of residence (40.0%). The infant mortality rate associated with congenital toxoplasmosis showed an increasing trend in the country in the years analysed. The spatial analysis showed heterogeneous distribution of mortality in the Brazilian territory and found no evidence of spatial autocorrelation; but spatial–temporal analysis identified three risk clusters involving 703 municipalities. Conclusion Infant mortality associated with congenital toxoplasmosis is a persistent public health problem in Brazil. The risk factors male sex, indigenous race/colour, early neonatal age, North and Northeast regions and risk clusters mapped in this study should be observed for future analysis and planning of health care policies in the control of infant deaths associated with congenital toxoplasmosis. Health surveillance strategies and public health policies need to be strengthened.