Polyetheretherketone (PEEK) is considered to be a promising bone implant material owing to its biocompatibility and elastic modulus, which is similar to that of natural bone. However, the clinical potential of PEEK is severely limited by its bioinertness, which leads to poor osseointegration, and the lack of antibacterial properties. In this study, the antimicrobial peptide, KR-12, was immobilized on the surface of PEEK implants with the assistance of polydopamine (PDA) to inhibit bacterial infection as well as to promote osteogenesis and osseointegration. Compared to unmodified PEEK, the PEEK with immobilized KR-12 showed significantly improved antibacterial activity against Staphylococcus aureus (ATCC 25923), both in vitro and in vivo. For the in vitro and in vivo evaluation of the osteogenic properties of modified PEEK, rat bone mesenchymal stem cells (rBMSCs) and a rat femoral defect model were used, respectively. The in vitro studies showed that compared to rBMSCs treated with unmodified PEEK, those treated with KR-12-coated PEEK exhibited improved adhesion, proliferation, and osteogenic differentiation. Moreover, micro-computed tomography and histological analysis suggested that the KR-12 coating promoted osteointegration in vivo in rat femurs. Taken together, these results suggest that the KR-12 coating could improve the antibacterial ability of pure or PDA-coated PEEK against Staphylococcus aureus (ATCC 25923), both in vitro and in vivo. Overall, KR-12 combined with the PDA film coating synergistically induced osteogenic effects both in vitro and in vivo. Thus, the surface-modified material, which exhibits both anti-bacterial and osteointegration properties, shows considerable potential for use as an orthopedic implant.