This paper proposes a semi-automatic Fontan surgery planning method for designing and manufacturing hemodynamically optimized patient-specific grafts. Fontan surgery is a palliative procedure for patients with a single ventricle heart defect by creating a new path using a vascular graft for the deoxygenated blood to be directed to the lungs, bypassing the heart. However, designing patient-specific grafts with optimized hemodynamic performance is a complex task due to the variety of patient-specific anatomies, confined surgical planning space, and the requirement of simultaneously considering multiple design criteria for vascular graft optimization. To address these challenges, we used parameterized Fontan pathways to explore patient-specific vascular graft design spaces and search for optimal solutions by formulating a nonlinear constrained optimization problem, which minimizes indexed power loss (iPL) of the Fontan model by constraining hepatic flow distribution (HFD), percentage of abnormal wall shear stress (%WSS) and geometric interference between Fontan pathways and the heart models (InDep) within clinically acceptable thresholds. Gaussian process regression was employed to build surrogate models of the hemodynamic parameters as well as InDep and [Formula: see text] (conduit model smoothness indicator) for optimization by pattern search. We tested the proposed method on two patient-specific models (n=2). The results showed the automatically optimized (AutoOpt) Fontan models hemodynamically outperformed or at least are comparable to manually optimized Fontan models with significantly reduced surgical planning time (15 hours versus over 2 weeks). We also demonstrated feasibility of manufacturing the AutoOpt Fontan conduits by using electrospun nanofibers.