AimsThis study aimed to explore the protective effects and possible mechanisms of baicalein on Aβ25–35-induced toxicity. Main methodsThioflavin-T (Th-T) dye was used to determine the effects of baicalein on Aβ25–35 aggregation in vitro. PC12 cells were stimulated with Aβ25–35, then the effects of baicalein on apoptosis, mitochondrial membrane potential (MMP), adenosine triphosphate (ATP), mitochondrial respiratory complex I, reactive oxygen species (ROS) and nitric oxide (NO) levels were determined. Moreover, LC-MS metabolomics approach was used to detect metabolic changes induced by baicalein in Aβ25–35-injured PC12 cells. Key findingsThe results showed that baicalein could inhibit the aggregation of Aβ25–35 in vitro. Furthermore, pretreatment with baicalein significantly prevented Aβ25–35-induced cell apoptosis, as manifested by increasing the levels of MMP, ATP and mitochondrial respiratory complex I, decreasing the contents of ROS and NO. LC-MS metabolomics revealed that baicalein can regulate 5 metabolites, mainly involving two metabolic pathways, arginine and proline metabolism, nicotinate and nicotinamide metabolism. SignificanceOur study revealed that baicalein has a protective effect on Aβ25–35-induced neurotoxicity in PC12 cells, which may be related to inhibition of apoptosis and metabolic disorders.