The molecular chaperone heat shock protein 90 (Hsp90) is highly expressed in tumor tissue according to many studies. However, there is no large-scale study investigating the expression of Hsp90 in pan-cancer so far, and the molecular mechanisms leading to aberrant Hsp90 expression are also largely unknown. To address these questions, we performed an in silico analysis of Hsp90 expression using mRNA sequencing data from The Cancer Genome Atlas study. The results were further validated using independent datasets. We found that the expression of HSP90AA1, a subtype of Hsp90, was much higher in hepatocellular carcinoma than in adjacent normal liver tissue. A large cancer panel with eight more cancer types revealed a similar trend except for prostate cancer, which had low HSP90AA1 expression in tumor tissue. Heat shock factor 1 followed a similar trend as HSP90AA1, with higher expression in cancer. HSP90AA1 expression was closely related to its copy numbers. Deletion of the HSP90AA1 locus in a subset of hepatocellular carcinoma led to low HSP90AA1 expression. In addition, higher HSP90AA1 expression was associated with poorer prognosis in hepatocellular carcinoma patients. In a multivariable analysis including tumor, node and metastasis stage, HSP90AA1 expression remained a negative prognostic factor, suggesting that the effect of HSP90AA1 was independent of tumor stage. In conclusion, we demonstrated that high HSP90AA1 expression was ubiquitous in cancer and that HSP90AA1 was a potential diagnostic and prognostic biomarker for hepatocellular carcinoma.