In this study, a novel porous hydroxyapatite scaffold was designed and fabricated to imitate natural bone through a multipass extrusion process. The conceptual design manifested unidirectional microchannels at the exterior part of the scaffold to facilitate rapid biomineralization and a central canal that houses the bone marrow. External and internal fissures were minimized during microwave sintering at 1,100 °C. No deformation was noted, and a mechanically stable scaffold was fabricated. Detailed microstructure of the fabricated artificial bone was examined by scanning electron microscope and X-ray diffractometer, and material properties like compressive strength were evaluated. The initial biocompatibility was examined by the cell proliferation of MG-63 osteoblast-like cells using MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) assay. Preliminary in vivo investigation in a rabbit model after 4 weeks and 8 weeks of implantation showed full osteointegration of the scaffold with the native tissue, and formation of bone tissue within the pore network, as examined by microcomputed tomography analyses and histological staining. Osteon-like bone microarchitecture was observed along the unidirectional channel with microblood vessels. These confirm a biomimetic regeneration model in the implanted bone scaffold, which can be used as an artificial alternative for damaged bone.