The manufacture of polyetheretherketone/hydroxyapatite (PEEK/HA) composites is seen as a viable approach to help enhance direct bone apposition in orthopaedic implants. A range of methods have been used to produce composites, including Selective Laser Sintering and injection moulding. Such techniques have drawbacks and lack flexibility to manufacture complex, custom-designed implants. 3D printing gets around many of the restraints and provides new opportunities for innovative solutions that are structurally suited to meet the needs of the patient. This work reports the direct 3D printing of extruded PEEK/HA composite filaments via a Fused Filament Fabrication (FFF) approach. In this work samples are 3D printed by a custom modified commercial printer Ultimaker 2+ (UM2+). SEM-EDX and µCT analyses show that HA particles are evenly distributed throughout the bulk and across the surface of the native 3D printed samples, with XRD highlighting up to 50% crystallinity and crystalline domains clearly observed in SEM and HR-TEM analyses. This highlights the favourable temperature conditions during 3D printing. The yield stress and ultimate tensile strength obtained for all the samples are comparable to human femoral cortical bone. The results show how FFF 3D printing of PEEK/HA composites up to 30 wt% HA can be achieved.