The acetyl-CoA pool has been identified using various cell measures in studies related to cell development and mitosis. It is suggested that acetyl-CoA elevates the level of histones at certain qualities of cell development. The relationship between ACOT12 and hepatocellular carcinoma (HCC) is unclear. Here, data on ACOT12 expression were obtained from HPA, GEPIA, TCGA portal, and UALCAN web repositories. Clinicopathological significance of ACOT12 was examined using Kaplan-Meier analysis, OncoLnc, TCGA portal and PROGgeneV2. The association between ACOT12 with cancer stem cells was examined based on GEO datasets GSE111802 and GSE7053. The link between ACOT12 and microRNAs and genes that modulate survival was determined based on Cytoscape, GEPIA, and TargetScan. These analyses revealed that relative to normal liver and paracancerous tissues, ACOT12 expression was downregulated in HCC and favorable liver tumors at both mRNA and protein levels. HCC patients with lower ACOT12 expression exhibited poorer overall and disease-free survival. Additionally, ACOT12 influenced HCC. In particular, low ACOT12 expression was related to the following groups of patients: poorly differentiated HCC, vascular invasion positive, sorafenib untreated, with alcohol consumption and hepatitis infection of HCC. The intersection of differentially expressed genes (DEGs) was examined to assess the underlying mechanism. This prompted the distinguishing proof of five possibly associated genes-GC, KNG1, DNAJC28, CUX2 and KMO. A network containing ACOT12 miR-7, miR-9, and miR-374b was constructed. Taken together, our findings indicate that ACOT12 is decreased in HCC and it might mediate HCC progression via stem cell-related genes.