Objective: To estimate premature mortality due to noncommunicable diseases (NCDs) in Brazilian municipalities. Methods: This ecological study estimated premature mortality rates due to cardiovascular diseases, chronic respiratory diseases, cancer and diabetes in Brazilian municipalities, for the three-year periods of 2010 to 2012 and 2015 to 2017, and it analyzed the spatial and temporal distribution of these rates. Data treatment combined proportional redistribution of the missing data and ill-defined causes, and the application of coefficients for under-registration correction. The local empirical Bayesian estimator was used to calculate municipal mortality rates. Results: Rates for the set of chronic diseases decreased in Brazil between the three-year periods. The mean rates for total NCDs declined in the South, Southeast and Central-West regions, remained stable in the North and increased in the Northeast. Mortality rates due to cardiovascular diseases were the highest in all regions but showed the greatest declines between the periods. Cancers were the second leading cause of death. The North and Northeast regions stood out as having increased mean rates of cancer between the periods analyzed and showing the highest mean premature mortality rates due to diabetes in the 2015 to 2017 period. Conclusion: Spatial and temporal distribution of premature mortality rates due to NCDs differed between Brazilian municipalities and regions in the three-year periods evaluated. The South and Southeast had decreased rates of deaths due to cardiovascular and chronic respiratory diseases, as well as diabetes. The North and Northeast had increased rates of deaths due to cancer. There was an increase in the rate of deaths due to diabetes in the Central-West.