Hepatocellular carcinoma (HCC) is a malignant tumor with rapid progression, high recurrence rate and poor prognosis. The objective of our investigation was to explore the prognostic value of CDK5R1 in HCC. The raw data of HCC raw data were downloaded from The Cancer Genome Atlas (TCGA) database. The Wilcoxon signed-rank test, Kruskal-Wallis test and logistic regression were applied to investigate the relevance between the CDK5R1 expression and clinicopathologic characteristics in HCC. Kaplan-Meier and Cox regression analysis were employed to examine the association between clinicopathologic features and survival. Gene set enrichment analysis (GSEA) was applied to annotate the biological function of CDK5R1. CDK5R1 was highly expressed in HCC tissues. The high expression of CDK5R1 in HCC tissues was significantly associated with tumor status (P=0.00), new tumor event (P=0.00), clinical stage (P=0.00), topography (P=0.00). Elevated CDK5R1 had significant correlation with worse overall survival (OS) (P=7.414e-04), disease-specific survival (DSS) (P=5.642e-04), disease-free interval (DFI) (P=1.785e-05), and progression-free interval (PFI) (P=2.512e-06). Besides, univariate and multivariate Cox regression analysis uncovered that increased CDK5R1 can independently predict adverse OS (P=0.037, hazard ratio [HR]=1.7 (95% CI [1.0-2.7])), DFI (P=0.007, hazard ratio [HR]=3.0 (95% CI [1.4-6.7])), PFI (P=0.007, hazard ratio [HR]=2.8 (95% CI [1.3-5.9])). GSEA disclosed that notch signaling pathway and non-small cell lung cancer were prominently enriched in CDK5R1 high expression phenotype. Increased CDK5R1 may act as a promising independent prognostic factor of poor survival in HCC. Copyright 2020 The Author(s).