Hepatic encephalopathy (HE) induced cognitive decline has long been associated with mitochondrial dysfunction. Therefore, the present study aimed to characterize mitochondrial alterations in HE and also examining the regulatory role of Sirtuins. Using both in vitro (NH4Cl induced SH-SY5Y) and in vivo (bile duct ligation, BDL) models, mitochondrial analysis revealed pronounced abnormalities, including reduced membrane potential, elevated oxidative stress, and swelling. Moreover, spatial memory was also significantly impaired in BDL rats. Following HE, nuclear Sirtuins (Sirtuin 1, 6, and 7) were significantly downregulated, whereas Sirtuin 2-5 remained largely unchanged. Reduced Sirtuin 1 expression in HE resulted in decreased occupancy at the HIF-1α promoter, diminishing transcriptional repression and leading to aberrant HIF-1α upregulation. Elevated HIF-1α in turn enhanced transcriptional activation of VDAC1 in both HE models. Pharmacological activation of Sirtuin 1 with SRT2104 suppressed HIF-1α levels reduced VDAC1 expression, while inhibition with EX-527 exhibited the reverse effect and worsened mitochondrial dysfunction. Furthermore, selective VDAC1 inhibition by VBIT-12 effectively restored mitochondrial integrity in NH4Cl-treated cells. In addition to the Sirtuin 1-HIF-1α mechanism, a separate regulatory pathway involving Sirtuin 6 was also uncovered. Loss of Sirtuin 6 amplified HIF-1α transcriptional activity by reducing its interaction with Sirtuin 6 and diminishing Sirtuin 6-mediated repression, thereby promoting increased expression of the downstream target VDAC1. Together, these observations identify reduced nuclear Sirtuin 1 and Sirtuin 6 as converging upstream regulators of the HIF-1α-VDAC1 axis, contributing to mitochondrial dysfunction in HE.