Fontan-associated liver disease leads to liver cirrhosis and hepatocellular carcinoma, worsening patient prognosis. Although the Model of End-Stage Liver Disease Excluding International Normalized Ratio score correlates with disease severity, precise prediction methods remain elusive. The hepatic computed tomography (CT) attenuation is used to assess steatohepatitis, which may offer insight into disease progression. This study aimed to determine the usefulness of hepatic CT attenuation values in assessing Fontan-associated liver disease progression. All post-Fontan patients with >20 years’ follow-up data between 1980 and 2021 were reviewed. We set five regions of interest with a 20-mm-diameter circle in the peripheral region of the liver to obtain minimum, maximum, mean, and standard deviation of the CT attenuation values, which were adjusted to those of the aorta. The impact of hepatic CT attenuation values on cirrhosis development was evaluated. Cox regression revealed significant associations between adjusted minimum (hazard ratio: 0.01 [0.00–0.02, p < 0.01), adjusted maximum (hazard ratio: 159 [4.34–5831, p < 0.01]), and standard deviation (hazard ratio: 1.89 [1.29–2.76, p < 0.01]) and Model of End-Stage Liver Disease Excluding International Normalized Ratio score (hazard ratio: 1.2 [1.02–1.43, p = 0.03]) with cirrhosis. In cirrhosis cases, the adjusted minimum value exhibited significant longitudinal alteration prior to cirrhosis (p < 0.01), whereas Model of End-Stage Liver Disease Excluding International Normalized Ratio scores remained stable. The hepatic CT attenuation values were associated with cirrhosis development and the longitudinal changes are more sensitive than the Model of End-Stage Liver Disease Excluding International Normalized Ratio score.