Objectives A novel Y-shaped baffle has been proposed for the Fontan operation with promising initial results. However, previous studies have relied either on idealized models or a single patient-specific model. The objective of this study is to comprehensively compare the hemodynamic performance and hepatic blood flow distribution of the Y-graft Fontan baffle with 2 current designs using multiple patient-specific models. Methods Y-shaped and tube-shaped grafts were virtually implanted into 5 patient-specific Glenn models forming 3 types of Fontan geometries: Y-graft, T-junction, and offset. Unsteady flow simulations were performed at rest and at varying exercise conditions. The hepatic flow distribution between the right and left lungs was carefully quantified using a particle tracking method. Other physiologically relevant parameters such as energy dissipation, superior vena cava pressure, and wall shear stress were evaluated. Results The Fontan geometry significantly influences the hepatic flow distribution. The Y-graft design improves the hepatic flow distribution effectively in 4 of 5 patients, whereas the T-junction and offset designs may skew as much as 97% of hepatic flow to 1 lung in 2 cases. Sensitivity studies show that changes in pulmonary flow split can affect the hepatic flow distribution dramatically but that some Y-graft and T-junction designs are relatively less sensitive than offset designs. The Y-graft design offers moderate improvements over the traditional designs in power loss and superior vena cava pressure in all patients. Conclusions The Y-graft Fontan design achieves overall superior hemodynamic performance compared with traditional designs. However, the results emphasize that no one-size-fits-all solution is available that will universally benefit all patients and that designs should be customized for individual patients before clinical application.