BACKGROUND: Clear cell renal cell carcinoma (ccRCC) is a lethal urological cancer that accounts for a considerable portion of all malignant tumors in adults. Alterations in mitochondrial function and metabolism may influence the onset and progression of ccRCC. This study aims to develop a novel clinical prognostic signature for ccRCC based on mitochondria-associated genes, as well as to identify new potential therapeutic agents for this condition. METHODS: A total of 539 ccRCC tumors and 72 normal kidney specimens were analyzed from The Cancer Genome Atlas (TCGA). We created a prognostic signature based on univariate, multivariate Cox, and least absolute shrinkage and selection operator (LASSO) Cox regression. A differential expression analysis, functional enrichment, and assessment of tumor immune cell infiltration were performed. Connectivity Map (CMap) and L1000CDS(2) dataset were utilized for potential therapeutic drug identification. Vorinostat was examined for its effects on ccRCC cell proliferation, cell death, migration, and invasion using Cell Counting Kit-8 (CCK-8), lactate dehydrogenase (LDH) release, wound healing, and transwell assays. RESULTS: The prognostic signature, comprising 16 mitochondria-related genes, demonstrated marked changes in overall survival between high- and low-risk groups. Functional analysis implicated immune-related pathways, indicating potential for immunotherapy strategies. Vorinostat, identified through drug screening, exhibited inhibitory implications on ccRCC cell proliferation, migration, and invasion and induced cell death. CONCLUSIONS: The constructed prognostic signature provides a valuable tool for patient prognosis prediction. Vorinostat emerges as a promising therapeutic candidate for high-risk ccRCC patients, contributing to a deeper understanding of ccRCC biology and personalized therapeutic interventions.