Fontan procedure is a surgical palliation used to treat patients with congenital heart disease such as single ventricle. Fenestration, a small hole between the conduit and right atrium, is expected to reduce the postoperative morbidity. Several recent studies have reported its effectiveness and favorable shapes. However, there is still no evidence on how the fenestration location influences three-dimensional hemodynamics in Fontan procedure. In this study, we constructed a three-dimensional patient specific model with fenestration based on the medical images. The three dimensional blood flow in Fontan Circulation is treated as laminar flow and computed by solution to the Navier-Stokes equations; boundary conditions based on zero-dimensional hemodynamic model specified for Fontan procedure are imposed at inlets and outlets. Our results indicate that locating the Fenestration in the middle of extra-cardiac conduit is the most effective way in terms of cardiac outputs and pressures.