Although liver fibrosis causes significant morbidity in the late postoperative period of the Fontan procedure, the diagnostic value of hyaluronic acid (HA), a serum marker of liver fibrosis, has not been established in Fontan patients. The purpose of this study was to determine whether increased serum HA concentration in Fontan patients is associated with an increase in inspiratory-to-expiratory flow rate ratio (Qin/Qex) of the portal vein (PV), which is indicative of liver fibrosis. We retrospectively studied 28 consecutive patients with Fontan circulation who underwent cardiac catheterisation for various indications. The median age at examination was 5.5 years (range 2.2–5.6). The median HA concentration was 17.7 ng mL⁻¹ (range 10.0–82.1), which was used to divide our 28 patients into two groups. Patients in the high-HA group had significantly greater Qin/Qex of the PV than those in the low-HA group (1.25 ± 0.12 vs. 1.12 ± 0.11, p < 0.05). Platelet counts were significantly lower in the high-HA group (216 ± 74 vs. 294 ± 104 × 10⁹ L⁻¹, p < 0.05). No significant difference was found in inferior vena caval pressure. In conclusion, increase of HA concentration in Fontan patients accompanies the change in PV hemodynamics peculiar to liver cirrhosis and might be an early indicator of liver fibrosis.