For univentricular heart patients, the Fontan circulation presents a unique pathophysiology due to chronic non-pulsatile low-shear-rate pulmonary blood flow, where non-Newtonian effects are likely substantial. This study evaluates the influence of non-Newtonian behavior of blood on fluid dynamics and energetic efficiency in pediatric patient-specific models of the Fontan circulation. We used immersed boundary-lattice Boltzmann method simulations to compare Newtonian and non-Newtonian viscosity models. The study included models from twenty patients exhibiting a low cardiac output state (cardiac index of 2 L/min/m2). We quantified metrics of energy loss (indexed power loss and viscous dissipation), non-Newtonian importance factors, and hepatic flow distribution. We observed significant differences in flow structure between Newtonian and non-Newtonian models. Specifically, the non-Newtonian simulations demonstrated significantly higher local and average viscosity, corresponding to a higher non-Newtonian importance factor and larger energy loss. Hepatic flow distribution was also significantly different in a subset of patients. These findings suggest that non-Newtonian behavior contributes to flow structure and energetic inefficiency in the low cardiac output state of the Fontan circulation.