Periodontitis, an infective disease caused by oral pathogens and the intrinsic aging process, results in the destruction of periodontal tissues and the loss of alveolar bone. This study investigated whether Boesenbergia pandurata extract (BPE) standardized with panduratin A exerted anti-periodontitis effects, using an aging model representative of naturally occurring periodontitis. In aged rats, the oral administration of BPE (200 mg·kg^-1·day^-1) for 8 weeks significantly reduced the mRNA and protein expression of interleukin-1β, nuclear factorkappa B, matrix metalloproteinase (MMP)-2, and MMP-8 in gingival tissues (p < 0.01). In alveolar bone, histological analysis with staining and micro-computed tomography revealed the attenuation of alveolar bone resorption in the BPE-treated aged group, which led to a significant reduction in the mRNA and protein expression of nuclear factor of activated T-cells c1 (NFATc1), c-Fos, tartrate-resistant acid phosphatase, and cathepsin K (p < 0.01). BPE not only increased the expression of osteoblast differentiation markers, such as alkaline phosphate, and collagen type I (COL1A1), but also increased the ratio of osteoprotegerin to RANKL. Collectively, the results strongly suggested that BPE is a natural resource for the prevention or treatment of periodontal diseases.