Portacaval anastomosis (PCA) is a model for hypometabolic liver dysfunction. Spongiform neurodegeneration has been detected in the cerebellum of PCA rats 13 weeks after surgery. This report characterizes the damage associated with spongiform degeneration by studying mitochondrial, ultrastructural, and oxidative changes in the molecular, Purkinje, and granular layers of the cerebellar cortex. Morphometry by electron microscopy determined an increase in mitochondrial presence in PCA rats. In parallel, mitochondria displayed smaller size, diminished interconnectivity, and decreased elongation. Fluorescent probes revealed that PCA cerebellar mitochondria showed a reduction in membrane potential (ΔΨ) alongside a rise in superoxide levels. In contrast, the calcium content exhibited variability across the three cerebellar layers. In addition, an elevation of intracellular reactive oxygen species in the cerebellar cortex was detected. The measurement of TBARS, conjugated dienes, and total antioxidant activity confirmed the presence of oxidative stress in the PCA cerebella. The increased number of smaller mitochondria was accompanied by an altered equilibrium between mitochondrial fission and fusion markers in PCA rats: increased FIS1 and p-DRP1, as well as OPA1, but decreased MFN1. Immunohistochemical analyses of these markers indicated that the molecular layer was the most affected in the cerebellum of PCA rats. In conclusion, we characterized the active cerebellar damage associated with dysregulated mitochondrial activity accompanied by an evident pro-oxidative condition. Ultrastructural analysis helped to strengthen the depiction of the mitochondrial and biochemical alterations associated with the spongiform vacuolization observed in the PCA cerebellar cortex, especially within the molecular layer.