Beta-secretase (BACE1) controls an essential step for the generation of amyloid- peptide (Aβ). As Aβ forms the principle pathologies in Alzheimer’s disease, lowering A production by inhibiting BACE1 is a plausible therapeutic approach. In the present study, we identified a natural polyphenol, luteolin, as a potent inhibitor of BACE1 transcription inhuman embryonic kidney 293 (HEK293) and human neuroblastoma (SH-SY5Y) cell lines. Luteolin is capable of suppressing the activation of BACE1 promoter by NF-κB signaling. We further characterized that luteolin interferes with NF-κB signaling by with both directly and indirectly disrupting p65 complex formation. In addition, we discovered that estrogen receptor mediates luteolin’s effect in inhibiting NF-κB signaling inhibiting and BACE1 transcription. Interestingly, the beneficial effects of luteolin may be attributed to selective activation profiles of luteolin to different estrogen receptor subtypes. Our study reports luteolin as a potent BACE1-inhibiting compound, providing useful information in understanding estrogen receptor- and NF-κB-mediated signaling and in regulating BACE1 expression.