A Fontan Y-shaped graft using a commercially available aortoiliac graft has been used to connect the inferior vena cava (IVC) to the pulmonary arteries. This modification of the Fontan procedure seeks to improve hepatic flow distribution (HFD) to the lungs. However, patient-specific anatomical restrictions might limit the space available for graft placement. Altering the superior vena cava (SVC) positioning is hypothesized to provide more space for an optimal connection, avoiding caval flow collision. Computational modeling tools were used to retrospectively study the effect of SVC placement on Y-graft hemodynamics. Patient-specific anatomies (N = 10 patients) and vessel flows were reconstructed from retrospective cardiac magnetic resonance (CMR) images after Fontan Y-graft completion. Alternative geometries were created using a virtual surgery environment, altering the SVC position and the offset in relation to the Y-graft branches. Geometric characterization and computational fluid dynamics simulations were performed. Hemodynamic factors (power loss and HFD) were computed. Patients with a higher IVC return showed less sensitivity to SVC positioning. Patients with low IVC flow showed varied HFD results, depending on SVC location. Balanced HFD values (50% to each lung) were obtained when the SVC lay completely between the Y-graft branches. The effect on power loss was patient specific. SVC positioning with respect to the Y-graft affects HFD, especially in patients with lower IVC flow. Careful positioning of the SVC at the time of a bidirectional Glenn (BDG) procedure based on patient-specific anatomy can optimize the hemodynamics of the eventual Fontan completion.