Increased life expectancy has led to an increase in the use of bone substitutes in numerous nations, with over two million bone-grafting surgeries performed worldwide each year. A bone defect can be caused by trauma, infections, and tissue resections which can self-heal due to the osteoconductive nature of the native extracellular matrix components. However, natural self-healing is time-consuming, and new bone regeneration is slow, especially for large bone defects. It also remains a clinical challenge for surgeons to have a suitable bone substitute. To date, there are numerous potential treatments for bone grafting, including gold-standard autografts, allograft implantation, xenografts, or bone graft substitutes. Tricalcium phosphate (TCP) and hydroxyapatite (HA) are the most extensively used and studied bone substitutes due to their similar chemical composition to bone. The scaffolds should be tested in vivo and in vitro using suitable animal models to ensure that the biomaterials work effectively as implants. Hence, this article aims to familiarize readers with the most frequently used animal models for biomaterials testing and highlight the available literature for in vivo studies using small and large animal models. This review summarizes the bio ceramic materials, particularly HA and β-TCP scaffolds, for bone defects in small and large animal models. Besides, the design considerations for the pre-clinical animal model selection for bone defect implants are emphasized and presented.