The deposition of amyloid-β (Aβ) peptides has been implicated as a one of pathological hallmark of Alzheimer's disease (AD). Increasing evidence indicates that Aβ initiates oxidative stress and a vicious cycle of mitochondrial damage, leading to apoptotic neuronal death. Pinocembrin (5,7-dihydroxyflavone), a major flavonoid found in honey and propolis, has shown significant neuroprotective property by suppressing Aβ cleaving enzyme in our previous study. The present study investigated a novel anti-AD effect of pinocembrin on mitochondrial dysfunction and apoptosis against Aβ injury. Neurotoxicity and apoptosis by Aβ were assessed and the underlying mechanism by which pinocembrin suppressed cell death, mitochondria dysfunction, caspase cascade and GSK-3β/Wnt/β-catenin signaling pathway related protein markers were evaluated in Aβ1-42-mediated PC12 cells. Pinocembrin significantly reversed Aβ-induced cell death, especially pinocembrin at 50 µM a similar neuroprotective effect to that of resveratrol, a well-known positive control. In addition, the compound counteracted Aβ‑induced mitochondrial dysfunction, which was supported by maintaining mitochondrial membrane potential, decreasing BAX protein, and increasing BCL‑2 protein within the mitochondria as well as upregulating TrxR1 mitochondrial antioxidant enzyme. Mitochondrial dysfunction by Aβ triggered the caspase cascade, whereas pinocembrin suppressed expression of caspase-9, -8 and -3. Interestingly, pinocembrin exerted neuroprotective effects against Aβ by inhibiting GSK-3β activation, which in turn promoted Wnt signaling via nuclear translocation of β‑catenin. Taken together, the present results demonstrated that pinocembrin prevented the Aβ-stimulated mitochondrial apoptosis via GSK-3β/Wnt/β-catenin signaling pathway, providing a useful approach for potential natural agent for AD prevention.