To systematically assess the effects of hydroxyapatite bone repair scaffold coated with bone morphogenetic protein-2 on murine calvarial defect models and to determine the quality of studies according to the Animal Research Reporting in In Vivo Experiments guidelines. Internet search was performed in duplicate using PubMed, MEDLINE, Ovid and Embase databases (without restrictions on publication date). The Animal Research Reporting in In Vivo Experiments guidelines were used to evaluate the quality of selected studies. Following screening, 12 studies were eligible for the review. Studies with average quality coefficients predominated (66.67%), followed by poor (25%) and excellent (8.33%) quality coefficients. Minimum quality scores were assigned to the Animal Research Reporting in In Vivo Experiments guideline items: housing and husbandry (9), allocation (11), outcomes (12), interpretation (18) and generalizability (19). Sprague–Dawley rats were the most frequently used (50%) species, and most studies had a sample size of more than 30 (58.33%). A defect dimension of 5 mm was the most common (33.33%). The biological hydroxyapatite composite scaffold was common (50%), and the bioactive factors were bone morphogenetic protein-2 (50%) and recombinant human bone morphogenetic protein-2 (50%). Histomorphometric results showed that bone morphogenetic protein-2 enhanced the capacity to regenerate bone considerably. In addition, scaffolds with bone morphogenetic protein-2 resulted in a significant increase in the blood vessel in the new bone. The findings suggested that data on animal experiments of hydroxyapatite scaffold coated with bone morphogenetic protein-2 in murine calvarial defect models lack homogeneity. Animal experiment should follow the Animal Research Reporting in In Vivo Experiments guidelines to promote the high quality, integrity and reproducibility. This systematic review suggested that bone morphogenetic protein-2 enhanced the capacity to regenerate bone and the angiogenesis in the new bone.