Intraatrial-conduit Fontan is considered a modification of both extracardiac and lateral-tunnel Fontan. In this study, the patient-specific hemodynamic performance of intraatrial-conduit and lateral-tunnel Fontan with fenestration, considered as conversion templates, was investigated based on the authors' patient cohort. Pulsatile computational fluid dynamics simulations were performed using patient-specific models of intraatrial-conduit and lateral-tunnel Fontan patients. Real-time "simultaneous" inferior and superior vena cava, pulmonary artery, and fenestration flow waveforms were acquired from ultrasound. Multiple hemodynamic performance indices were investigated, with particular focus on evaluation of the pulsatile flow performance. Power loss inside the lateral-tunnel Fontan appeared to be significantly higher than with the intraatrial-conduit Fontan for patient-specific cardiac output and normalized connection size. Inclusion of the 4-mm fenestration at a 0.24 L/min mean flow resulted in a lower cavopulmonary pressure gradient and less time-averaged power loss for both Fontan connections. Flow structures within the intraatrial conduit were notability more uniform than within the lateral tunnel. Hepatic flow majorly favored the left lung in both surgical connections: conversion from lateral-tunnel to intraatrial-conduit Fontan resulted in better hemodynamics with less power loss, a lower pressure gradient, and fewer stagnant flow zones along the conduit. This patient-specific computational case study demonstrated superior hemodynamics of intraatrial-conduit Fontan over those of lateral-tunnel Fontan with or without fenestration and improved performance after conversion of the lateral tunnel to the intraatrial conduit. The geometry-specific effect of the nonuniform hepatic flow distribution may motivate new rationales for the surgical design.