BACKGROUND: Hepatocellular carcinoma (HCC) is a highly prevalent malignancy with poor prognosis. Endothelial cells (ECs) play a crucial role in HCC progression, yet their involvement at the single-cell level remains underexplored. This study aimed to identify ECs-specific markers and develop a prognostic multi-gene signature for HCC using single-cell RNA sequencing (scRNA-seq). MATERIALS AND METHODS: Single-cell transcriptomic data from 12 HCC samples were analyzed to identify EC-associated genes. A prognostic gene signature was constructed using Lasso-Cox regression analysis based on The Cancer Genome Atlas (TCGA) cohort and subsequently validated using an independent cohort from the International Cancer Genome Consortium (ICGC). Immunohistochemistry (IHC) and Western blotting were employed to experimentally validate gene expression in tissue samples. RESULTS: Five EC-specific genes-NDRG1, HBEGF, FKBP1A, KLRB1, and FDPS-were identified as prognostic markers. The resulting multi-gene signature effectively stratified patients into high- and low-risk groups, with significant differences in overall survival. Validation in the ICGC cohort confirmed the model's predictive performance. IHC and Western blotting results further confirmed the elevated expression of these genes in HCC tissues. CONCLUSIONS: This study established an EC-related prognostic signature that accurately predicts HCC prognosis. The identified markers may aid early diagnosis and serve as potential therapeutic targets for HCC treatment.