The use of polyetheretherketone (PEEK) has grown exponentially in the biomedical field in recent decades because of its outstanding biomechanical properties. However, its lack of bioactivity/osteointegration remains an unresolved issue toward its wide use in orthopedic applications. In this work, graphene nanosheets have been incorporated into PEEK to obtain multifunctional nanocomposites. Because of the formation of an electrical percolation network and the π-π* conjugation between graphene and PEEK, the resulting composites have achieved 12 orders of magnitude enhancement in their electrical conductivity and thereby enabled electrophoretic deposition of a bioactive/antibacterial coating consisting of stearyltrimethylammonium chloride-modified hydroxyapatite. The coated composite implant shows significant boosting of bone marrow mesenchymal stem cell proliferation in vitro. In addition, the strong photothermal conversion effect of the graphene nanofillers has enabled laser-induced heating of our nanocomposite implants, where the temperature of the implant can reach 45 °C in 150 s. The unique multifunctionality of the implant has also been demonstrated for photothermal applications such as enhancing bacterial eradication and tumor cell inhibition, as well as bone tissue regeneration in vivo. The results suggest the strong potential of our multifunctional implant in bone repair applications as well as multimodal therapy of challenging bone diseases such as osteosarcoma and osteomyelitis.