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Summary: Background: While surveillance improves the early detection of hepatocellular carcinoma (HCC), it is unclear whether this has improved prognosis in clinical practice. Aims: To investigate the characteristics and prognoses of patients with viral versus non‐viral HCC over the previous two decades in Japan, while HCC surveillance has been active. Methods: This multi‐centre study enrolled 6007 patients initially diagnosed with HCC between 2000 and 2020 at seven high‐volume academic centres. Patients were categorised based on dates of diagnosis: 2000–2006, 2007–2013 and 2014–2020. HCC characteristics and post‐diagnosis survival rates were compared between periods in patients with viral and non‐viral HCC. Results: The percentage of patients with non‐viral HCC increased during the study period. The maximal tumour size and percentage of patients with multinodular HCC decreased significantly over time in the viral HCC group but remained unchanged in the non‐viral HCC group. Liver function at diagnosis improved over time in both groups, but to a greater extent in the viral HCC group. Survival rates increased significantly with time in the viral HCC group, but not in the non‐viral HCC group. Conclusions: The prevalence of non‐viral HCC is increasing. Although the survival of patients with viral HCC improved significantly over the past two decades, there was no improvement in patients with non‐viral HCC. This was presumably due mainly to lower surveillance among patients with non‐viral HCC and failure to diagnose early‐stage HCC. [ABSTRACT FROM AUTHOR]