Background. Chagas disease (CD) is associated with excess mortality in infected people in endemic countries, but little information is available in non-endemic countries. The aim of the study was to analyze mortality in patients admitted to the hospital with CD in Spain. Methods. A retrospective, observational study using the Spanish National Hospital Discharge Database. We used the CD diagnostic codes of the 9th and 10th International Classification of Diseases to retrieve CD cases from the national public registry from 1997 to 2018. Results. Of the 5022 hospital admissions in people with CD, there were 56 deaths (case fatality rate (CFR) 1.1%, 95% confidence interval (CI) 0.8%, 1.4%), 20 (35.7%) of which were considered directly related to CD. The median age was higher in those who died (54.5 vs. 38 years; p < 0.001). The CFR increased with age, peaking in the 70–79-year (7.9%, odds ratio (OR) 6.27, 95% CI 1.27, 30.90) and 80–89-year (16.7%, OR 14.7, 95% CI 2.70, 79.90) age groups. Men comprised a higher proportion of those who died compared to survivors (50% vs. 22.6%; p < 0.001). Non-survivors were more likely to have neoplasms (19.6% vs. 3.4%; p < 0.001), heart failure (17.9% vs. 7.2%; p = 0.002), diabetes (12.5% vs. 3.7%; p = 0.001), chronic kidney failure (8.9% vs. 1.6%; p < 0.001), and HIV (8.9% vs. 0.8%; p < 0.001). In the multivariable analysis, the variables associated with mortality were age (adjusted OR (aOR) 1.05; 95% CI: 1.03, 1.07), male sex (aOR 1.79, 95% CI 1.03, 3.14), cancer (aOR: 4.84, 95% CI 2.13, 11.22), and HIV infection (aOR 14.10 95% CI 4.88, 40.73). Conclusions. The case fatality rate of CD hospitalization was about 1%. The mortality risk increased with age, male sex, cancer, and HIV infection.