Abnormal tau modifications are one of the main contributors to neurodegenerative processes present during Alzheimer's disease (AD). In this context, truncated tau by caspase-3, a pathological tau form, affects mitochondrial function and antioxidant regulation, contributing to synaptic and cognitive impairment in AD mouse models. We previously showed that the presence of caspase-3 cleaved tau promotes mitochondrial impairment in neuronal cells, where Cyclophilin-D (CypD) protein could be a crucial element. CypD is considered the master regulator of mitochondrial permeability transition pore (mPTP) opening, and its ablation prevents neurodegenerative and cognitive damage induced by β-amyloid in mouse models of AD. However, the possible role of CypD in the neurodegenerative processes mediated by caspase-3-cleaved tau has not been explored. Here, we use tau (-/-) and CypD (-/-) knock-out mice that were subjected to right-side hippocampal stereotaxic injection to induce GFP (AAV-Syn-GFP), full-length (AAV-Syn-GFP-T4) or caspase-3-cleaved (AAV-Syn-GFP-T4C3) tau expression. Then, cognitive performance, synaptic architecture, and hippocampal mitochondrial function were evaluated two months later. We observed that caspase-3 cleaved tau expression inducing cognitive decline, vesicle and synaptic protein deregulation, and mitochondrial impairment generated by the mPTP opening. More interestingly, when caspase-3 cleaved tau was expressed in the hippocampus of CypD (-/-) mice, cognitive decline, synaptic impairment, and mitochondrial damage mediated by mPTP were prevented, demonstrating a novel role of CypD in neurodegenerative changes induced by truncated tau in AD.