Berberrubine (BRB), belonging to the benzylisoquinoline alkaloid, is a main metabolite of berberine in vivo. BRB was previously proven to undergo metabolic activation mediated by P450s. In this study, the chemical interactions between BRB and CYP2D6 enzyme were investigated. First, a variety of P450s participated in the metabolism of berberine transformed to BRB, but CYP2D6 was the most involved enzyme. A time-, concentration-, and nicotinamide adenine dinucleotide phosphate (NADPH)-dependent inhibition of CYP2D6 was caused by BRB. The inhibitory effect of BRB on CYP2D6 was irreversible. The maximum reaction rate constants of inactivation (kinact) and half-maximal inactivation (KI) of BRB on CYP2D6 were 0.0410 min-1 and 3.798 μM, respectively. Metoprolol, a classic substrate of CYP2D6, attenuated CYP2D6 from inactivation by BRB. Glutathione (GSH) and catalase/superoxide dismutase failed to protect against the inactivation of CYP2D6 caused by BRB. Three cys-based adducts derived from the reaction of electrophilic metabolites of BRB with CYP2D6 were detected by ultra performance liquid chromatography-mass spectrometry (UPLC-MS)/MS. The reactive metabolites derived from BRB might be responsible for the inactivation of CYP2D6. In summary, BRB was characterized as a mechanism-based inactivator of CYP2D6.