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Berberis species are known for their use in traditional medicine. Here, we report the phenolic composition and bioactivity of methanolic and aqueous extracts of Berberis thunbergii DC. leaves. The phenolic profiling and the quantitation of the main compounds were performed by high-performance liquid chromatography with diode array and mass spectrometry detections. The most abundant compounds in both extracts were caffeoylquinic acids (chlorogenic acid, particularly, with a concentration of 90.1–101.3 mg g−1 dried extract), followed by caffeoylglucaric acids and quercetin glycosides. Antioxidant and radical scavenging assays (phosphomolybdenum, DPPH, ABTS, CUPRAC, FRAP, metal chelating activity), as well as enzyme inhibitory assays (acetylcholinesterase, butyrylcholinesterase, tyrosinase, amylase, glucosidase, and lipase), were carried out to evaluate the potential bioactivity of B. thunbergii. The methanolic extract presented the highest antioxidant and radical scavenging values, in agreement with its higher phenolic content. Regarding enzyme inhibitory potential, the methanolic extract was also more potent than the aqueous one. Hence, B. thunbergii leaves represent a suitable candidate for the preparation of pharmaceutical or nutraceutical products.