Three-dimensional computational fluid dynamics (CFD) simulations were performed in the anastomotic region of the Fontan route between the venae cava and pulmonary arteries to investigate the risk of thrombosis due to blood stasis in the Fontan circulation. The finite volume method based on the time-averaged continuity and Navier–Stokes equations combined with the k-ω SST turbulent model was used in the CFD simulations. Low shear rate (SR) and SR on the wall (WSR) of <10 s−1 were used as markers to assess blood stasis as a cause of blood coagulation. Simulated blood flow velocity and both SR and WSR were reduced in the right atrium (RA) as the cavity of a flow channel in the atriopulmonary connection (APC) Fontan model, whereas the values increased in the total cavopulmonary connection (TCPC) Fontan model, which has no cavity. The volume of SR <10 s−1 and wall surface area of WSR <10 s−1 were, respectively, 4.6–261.8 cm3 and 1.2–38.3 cm2 in the APC Fontan model, and 0.1–0.3 cm3 and 0.1–0.6 cm2 in the TCPC Fontan model. The SR and WSR increased in the APC model with a normal-sized RA and the TCPC model as the flow rate of blood from the inferior vena cava increased with exercise; however, the SR and WSR in the RA decreased in the APC model with a dilated RA owing to the development of a recirculating flow. These findings suggest that the APC Fontan has a higher risk of thrombosis due to blood stasis than the TCPC Fontan and a higher RA dilation is associated with a higher risk of thrombosis from a fluid mechanics perspective.