Background: In Brazil, acute Chagas disease (ACD) surveillance involves mandatory notification, which allows for population-based epidemiological studies. We conducted a nationwide population-based ecological analysis of the spatiotemporal patterns of ACD notifications in Brazil using secondary surveillance data obtained from the Notifiable Diseases Information System (SINAN) maintained by Brazilian Ministry of Health. Methodology/Principal findings: In this nationwide population-based ecological all cases of ACD reported in Brazil between 2001 and 2018 were included. Epidemiological characteristics and time trends were analyzed through joinpoint regression models and spatial distribution using microregions as the unit of analysis. A total of 5,184 cases of ACD were recorded during the period under study. The annual incidence rate in Brazil was 0.16 per 100,000 inhabitants/year. Three statistically significant changes in time trends were identified: a rapid increase prior to 2005 (Period 1), a stable drop from 2005 to 2009 (Period 2), followed by another increasing trend after 2009 (Period 3). Higher frequencies were noted in males and females in the North (all three periods) and in females in Northeast (Periods 1 and 2) macroregions, as well as in individuals aged between 20–64 years in the Northeast, and children, adolescents and the elderly in the North macroregion. Vectorial transmission was the main route reported during Period 1, while oral transmission was found to increase significantly in the North during the other periods. Spatiotemporal distribution was heterogeneous in Brazil over time. Despite regional differences, over time cases of ACD decreased significantly nationwide. An increasing trend was noted in the North (especially after 2007), and significant decreases occurred after 2008 among all microregions other than those in the North, especially those in the Northeast and Central-West macroregions. Conclusions/Significance In light of the newly identified epidemiological profile of CD transmission in Brazil, we emphasize the need for strategically integrated entomological and health surveillance actions.