This case report describes two patients with congenital heart disease (CHD) who underwent Fontan palliation surgery in their youth and subsequently developed Fontan-associated liver disease (FALD) in adulthood. While undergoing routine screening for hepatocellular carcinoma (HCC), both patients had significantly elevated serum alpha-fetoprotein testing and diagnostic radiographic findings consistent with early-stage HCC. At the same academic medical centre, both patients were treated with localised yttrium-90 (Y90) radioembolisation therapy, and neither underwent liver transplantation (LT). After Y90 radioembolisation, both patients achieved HCC remission that has sustained at 3 years post-treatment. These cases suggest that Y90 radioembolisation may offer effective, transplant-free management of HCC in selected FALD patients. Given the growing adult FALD population, further studies are needed to guide surveillance and identify predictors of response to non-surgical therapies.