Background: Down syndrome (DS) is considered a risk factor for mortality associated with the Fontan operation. The objective was to show the contemporary short-term outcome of the Fontan operation for a functionally univentricular heart in patients with DS and non-DS, along with an analysis of significant predictors for in-hospital mortality. Methods: This was a retrospective study using The Society of Thoracic Surgeons Congenital Database to assess in-hospital mortality and its predictors in patients with DS and non-DS undergoing the Fontan operation over 16 years (2001-2016). The primary outcome was in-hospital mortality. Statistical analysis was performed using univariable and multivariable logistic regression models. Results: Our study cohort consisted of 12,074 patients (81 DS and 11,993 non-DS). The overall in-hospital mortality rate significantly improved in the recent era (2009-2016): 2.4% to 1.3%, P <.001. The DS group had a higher in-hospital mortality rate (12.3% vs 1.6%, P <.001) with an odds ratio of 8.6 (95% confidence interval, 4.4-17.0). The DS group had a higher 30-day mortality rate, a longer median postoperative length of stay, and a higher incidence of postoperative complications. The multivariable model showed that DS was the strongest predictor of in-hospital mortality, with an odds ratio of 11.6 (95% confidence interval, 5.1-26.4), adjusted for other significant variables including era effect, weight, and primary cardiac diagnosis. Conclusions: The in-hospital mortality for the Fontan operation significantly improved in the contemporary era. DS was a significant risk factor for in-hospital morbidity and mortality associated with the Fontan operation.