Background: There is a long history of segregation in the U.S.A with enduring impacts on cancer outcomes today. We evaluated the impact of segregation on racial disparities in Hepatocellular Carcinoma (HCC) treatment and outcomes. Methods: We obtained data on black and white patients with HCC from the SEER program (2005–2015) within the 100 most populous participating counties. Our exposure was the index of dissimilarity (IoD), a validated measure of segregation. Outcomes were overall survival, advanced stage at diagnosis (Stage III/IV) and surgery for localized disease (Stage I/II). Cancer-specific survival was assessed using Kaplan–Meier estimates. Results: Black patients had a 1.18 times increased risk (95%CI 1.14,1.22) of presenting at advanced stage as compared to white patients and these disparities disappeared at low levels of segregation. In the highest quartile of IoD, black patients had a significantly lower survival than white (17 months vs 27 months, p < 0.001), and this difference disappeared at the lowest quartile of IoD. Conclusions: Our data illustrate that structural racism in the form racial segregation has a significant impact on racial disparities in the treatment of HCC. Urban and health policy changes can potentially reduce disparities in HCC outcomes.