Objective: To investigate the expression of FK506 binding protein 5 (FKBP5) in hepatocellular carcinoma (HCC) and its clinical significance. Methods: The expressions of FKBP5 mRNA and protein in 30 fresh HCC and the adjacent tissue paired samples were determined by RT-PCR and Western blot, respectively. Then, immunohistochemical staining was performed in paraffin-embedded specimens from 107 HCC patients and the relations of FKBP5 expression with clinicopathologic features and prognosis of HCC patients were analyzed. Results: Of the 30 fresh HCC tissues, 26 samples (86.7%) showed that the FKBP5 mRNA expression level was markedly higher in HCC tissue than that in its adjacent tissue, and FKBP5 protein expression level in HCC tissue was also markedly increased compared with adjacent normal tissue. In the 107 paraffin-embedded specimens, the high expression rate of FKBP5 protein in HCC tissues was significantly higher than that in adjacent tissues (63.6% vs. 28.0%, P<0.001); high FKBP5 expression was significantly associated with tumor size (P=0.009), lesion number (P=0.018), microvascular invasion (P=0.020), TNM stage (P=0.009) and BCLC stage (P=0.024); both overall survival rate and disease-free survival rate in patients with high FKBP5 expression were significantly lower than those in patients with low FKBP5 expression (both P<0.001); high FKBP5 expression was an independent risk factor for either overall survival (HR=1.992, 95% CI=1.127–3.522, P=0.018) or disease-free survival (HR=1.787, 95% CI=1.067–2.992, P=0.027). Conclusion: FKBP5 expression is increased in HCC tissue, and its overexpression is associated with unfavorable clinicopathologic features and poor prognosis of HCC patients, suggesting that FKBP5 may be a potential prognostic indicator for HCC.