Autogenous bone grafts are still the criterion standard treatment option in critical-size bone defect reconstructions, and many therapies can affect its incorporation. In this study, it was aimed to research the effects of desferroxamine (DFO) application on bone and bone graft healing due to the effects of osteoblast and osteoclast regulation and stimulation of angiogenesis. Rat zygomatic arch critical-size bone defect model (5 mm) was used as the experimental model. Thirty-two Sprague-Dawley rats (64 zygomatic arches) were divided into 4 groups (16 zygomatic arches in each). In groups 1 and 2, defects were reconstructed with the bone grafts harvested from the other side, and the right arc was named as group 1, and the left was group 2. At group 1, 200 μM/300 μL dosage of DFO was injected at the zygomatic arch region starting at the seventh day preoperatively and lasting until the 45th day postoperatively. Group 2 animals were defined as the control group of group 1, and 0.9% NaCl injection was applied. In groups 3 and 4, there was no repair after the formation of defects, and the right arc region was treated with DFO, and left was treated with 0.9% NaCl for postoperative 45 days, respectively. Radiological (computed tomography), histological (hematoxylin-eosin), and biomechanical (3-point bending test) tests were used for the evaluation. In radiological evaluation, there was a statistically significant decrease (P < 0.05) in bone defect size in group 3 animals at the 4th, 8th, and 12th weeks, and bone graft volume showed a statistical difference at all weeks (P < 0.05). In histological evaluation, it was observed that there was an increase in osteoblast number and vascularity rates (P < 0.05) in the DFO-treated groups at all weeks. Biomechanical evaluation of the subjects showed increase in bone strength in group 1 animals at 12 weeks. In this study, it was shown that DFO treatment increased bone graft incorporation and healing in critical-size bone defects. In this aspect, we suggest that DFO can be used to increase graft incorporation in risky areas and reduce the defect size in patients who are not suitable for vascularized bone graft transfer.