Research indicated that berberine (BBR) plays a protective role in modulating Alzheimer's disease (AD). This study aimed to explore the target genes of BBR associated with AD therapy using a network pharmacology study. Through network pharmacology analysis, two main potential target genes, β-amyloid precursor protein (APP) and peroxisome proliferator-activated receptor gamma (PPARG), of BBR for AD therapy were screened out. Further experiments demonstrated that BV2 and C8-D1A treated with BBR were decreased in the mRNA and protein expression of APP and presenilin 1 while PPARG was increased with a reduction in the NF-κB pathway. A similar result was shown in vivo. Through a network pharmacology study, this study supported that BBR played a protective role in the AD mice model via blocking APP processing and amyloid plaque formation. It also promotes PPARG expression to blockage of NF-κB pathway-mediated inflammatory response and neuroinflammation.