Carbonate apatite (CO3Ap) block can be used as a bone substitute because it can be remodeled to new natural bone in a manner conforming with the bone remodeling process. Among the many porous structures available, honeycomb (HC) structure is advantageous for rapid replacement of CO3Ap to bone. In this study, the feasibility to fabricate a CO3Ap HC was studied, along with its initial tissue response in rabbit femur bone defect. First, a mixture of Ca(OH)2 and a wax‐based binder was extruded from a HC mold. Then the fabricated HC was heated for binder removal and carbonation at 450°C in a mixed O2–CO2 atmosphere, forming a CaCO3 HC. When the CaCO3 HC was immersed in 1 mol/L Na3PO4 solution at 80°C for 7 days, its composition changed from CaCO3 to CO3Ap, maintaining the structure of the original CaCO3 HC. Compressive strengths of the CaCO3 and CO3Ap HCs were 65.2 ± 7.4 MPa and 88.7 ± 4.7 MPa, respectively. When the rabbit femur bone defect was reconstructed with the CO3Ap HC, new bone penetrated the CO3Ap HC completely. Osteoclasts and osteoblasts were found on the surface of the newly formed bone and osteocytes were also found in the newly formed bone, indicating ongoing bone remodeling. Furthermore, blood vessels were formed inside the pores of CO3Ap HC. Therefore, CO3Ap HC has good potential as an ideal bone substitute. © 2019 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 107A: 1014–1020, 2019.