Background: The demographic shift and epidemiologic transition in Brazil have drawn attention to ways of measuring population health that complement studies of mortality. In this paper, we investigate regional differences in healthy life expectancy based on information from the National Health Survey (PNS), 2013. Methods: In the survey, a three-stage cluster sampling (census tracts, households and individuals) with stratification of the primary sampling units and random selection in all stages was used to select 60,202 Brazilian adults (18 years and over). Healthy life expectancies (HLE) were estimated by Sullivan’s method according to sex, age and geographic region, using poor self-rated health for defining unhealthy status. Logistic regression models were used to investigate socioeconomic and regional inequalities in poor self-rated health, after controlling by sex and age. Results: Wide disparities by geographic region were found with the worst indicators in the North and Northeast regions, whether considering educational attainment, material deprivation, or health care utilization. Life expectancy at birth for women and men living in the richest regions was 5 years longer than for those living in the less wealthy regions. Modeling the variation across regions for poor self-rated health, statistically significant effects (p < 0.001) were found for the North and Northeast when compared to the Southeast, even after controlling for age, sex, diagnosis of at least one non-communicable chronic disease, and schooling or socioeconomic class. Marked regional inequalities in HLE were found, with the loss of healthy life much higher among residents of the poorest regions, especially among the elderly. Conclusions: By combining data on self-rated health status and mortality in a single indicator, Healthy Life Expectancy, this study demonstrated the excess burden of poor health experienced by populations in the less wealthy regions of Brazil. To mitigate the effects of social exclusion, the development of strategies at the regional level is essential to provide health care to all persons in need, reduce risk exposures, support prevention policies for adoption of healthy behaviors. Such strategies should prioritize population groups that will experience the greatest impact from such interventions.