Budd-Chiari syndrome (BCS) can be incidentally complicated by hepatocellular carcinoma (HCC), thereby decreasing the survival of these patients. Our study aims to systematically review the prevalence and risk factors of HCC in BCS patients. A PubMed search was performed to identify all original articles that reported the prevalence and risk factors of HCC in BCS patients. Primary items were the prevalence and risk factors of HCC in BCS patients. Of 1487 articles identified, 16 were included in our study. The prevalence of HCC in BCS is 2.0-46.2% in 12 Asian studies, 40.0-51.6% in two African studies, 11.3% in one European study, and 11.1% in one American study. Irrespective of hepatitis as the underlying risk factor of HCC, the pooled prevalence of HCC was 17.6% in BCS patients [95% confidence interval (CI): 10.1-26.7%], 26.5% in inferior vena cava obstruction (95% CI: 14.4-40.7%), and 4.2% in hepatic vein obstruction (95% CI: 1.6-7.8%). As patients with HCC and concomitant hepatitis were excluded, the pooled prevalence of HCC was 15.4% in BCS patients (95% CI: 6.8-26.7%). Heterogeneity among studies was statistically significant in these meta-analyses. The risk factors of HCC in BCS included hepatic venous pressure gradient and female sex in two Asian studies, and male sex, factor V Leiden mutation, and inferior vena cava obstruction in one European study. HCC was frequent in BCS. However, there was a huge variation among studies. Routine surveillance for HCC is warranted in BCS patients. The risk factors of HCC in BCS may vary depending on the geographic origin of the studies.