Introduction Market estimates show that the bone replacement market is estimated to reach USD4.94 billion by 2030, within the orthopaedic, oral and maxillofacial reconstructive sectors. Statistics provided by National Center for Biotechnology Information, estimated that in 2015 around 7 million people underwent bone replacement procedures in America. According to the World Health Organization, between 2010 and 2050, the geriatric population in developing and developed countries is projected to increase by 250% and 71%, respectively. Currently, conventional reconstructive techniques for bone defects are challenging, and the limitations associated with donor site availability and morbidities demands clinically translatable alternatives, including scaffold guided bone tissue engineering (SGBTE) approaches. Irrespective of the numerous scaffold designs that have been investigated in the last 30 years, the number of SGBTE approaches reaching clinical application are limited. Amongst the hurdles to meet patient-specific needs, one of the greatest challenges for a SGBTE device to reach the clinic lies with the USA Federal Food and Drug Administration (FDA) regulatory approval. Biocompatibility with human tissues and a history of well-established and standardized pre-clinical models is an essential condition to acquire FDA consent. To thoroughly mimic human in vivo conditions, and to evaluate the effects of SGBTE on critical-sized bone defect regeneration, several large animal models have been developed. Amongst the pre-clinical models published so far, most of them are not well devised, described, and standardized and therefore remain challenging to replicate and to translate into clinical settings. Here we describe our well-established sheep animal model as a pre-clinical tool for evaluating SGBTE. Methodology A comprehensive set of procedures to establish a critical-sized bone defect in a sheep model is provided by following four steps: (i) preoperative planning and preparation, (ii) surgical approach, (iii) postoperative management, and (iv) post-mortem analysis. Results Several studies have been undertaken using this protocol, including a variety of SGBTE concepts in combination with autologous bone grafts, autologous and allogenic mesenchymal bone marrow precursor, platelet rich plasma, and bone morphogenic proteins. Most studies utilised medical grade polycaprolactone scaffolds. Replication of this protocol for peer-reviewed publications can be achieved within two year. Conclusion Although the use of large animal models has been recommended by the FDA, performing in vivo pre-clinical studies using large animal models, entails high costs and are dependent on a lengthy list of factors prior to full pre-market approval. Since large financial costs are required for advancing clinical trials, pre-clinical research entails narrowing numerous novel treatments and acquiring reliable evidence of a treatment’s clinical utility in a proxy species. Sheep are amongst the most suitable large animal model recapitulating human load-bearing conditions, a major requirement for scaffold translation into clinical settings. The use of well-established and clinically-relevant models combined with thorough, reproducible surgical and post-explanation analysis enables us to produce strong scientific data which in turn enables direct comparison between different treatment options for critical-sized defect repair – a shortfall with other less established models. Finally, it offers the ability to improve human predictability, mapping biomaterial’s degradation and can address longevity of therapeutic benefit.