Apical periodontitis (AP), an inflammatory lesion around the apex of tooth roots, is mostly caused by dental pulp infection. Proprotein convertase subtilisin/kexin type 9 (PCSK9) plays a vital role in regulating cholesterol homeostasis by targeting low-density lipoprotein receptor (LDLR) and participates in bacterium-induced chronic periodontitis. However, the roles of PCSK9 in AP are unknown. Here, we investigated its role in AP by using Pcsk9-/- mice. Micro-computed tomography scanning and histological staining revealed that the periapical bone loss of Pcsk9-/- mice was greater than that of wild-type (WT) mice, and increased expression of inflammation-related factors tumor necrosis factor α (TNF-α) and interleukin (IL)-6 was also observed. Immunofluorescence staining and quantitative real-time polymerase chain reaction showed PCSK9 expression in bone marrow macrophages (BMMs) was increased after treatment with lipopolysaccharide (LPS). This finding was consistent with the in vivo results that the expression level of PCSK9 in exposed WT mice increased compared with that in unexposed WT mice. After LPS challenge, the expression levels of TNF-α, IL-1β, and IL-6 in BMMs were increased, and Pcsk9 knockout aggravated the expression of these inflammatory factors. The number of osteoclasts positive for tartrate-resistant acid phosphatase staining around the apical lesion in Pcsk9-/- mice was higher than that in WT mice. Then BMMs underwent the osteoclast differentiation. Pcsk9 knockout BMMs induced increased and larger osteoclasts. While this effect of Pcsk9 knockout was abolished by the addition of Ldlr small interfering RNA, revealing that Pcsk9 knockout increased osteoclastogenesis was dependent on the LDLR. Immunohistochemistry staining showed increased expression level of LDLR in exposed Pcsk9-/- periapical areas. In vitro experiments showed that LPS promoted the expression level of LDLR in Pcsk9-/- BMMs and increased osteoclast formation ability, indicating that LPS promoted the elevation of osteoclasteogenesis caused by the Pcsk9 knockout. In conclusion, Pcsk9 deficiency aggravated the inflammatory response and promoted the osteoclastogenesis in an LDLR-dependent manner in AP experimental mice.