Bone graft techniques are used to compensate for bone loss in areas with deficient regeneration. However, matrix metalloproteases (MMPs) can limit bone formation by degrading extracellular matrices, which are required for bone regrowth. Noteworthily, rutin is a natural flavonoid compound that inhibits the genetic expression of various MMPs. Therefore, rutin may serve as an inexpensive and stable alternative to the growth factors used to accelerate dental bone graft healing. This study aimed to evaluate the potential of mixing rutin gel with allograft bone to accelerate the healing of bone defects in an in vivo rabbit model. Bone defects were surgically induced in New Zealand rabbits (n= 3 per group) and subsequently treated with bone grafts along with rutin or control gel. Overall, treatment with rutin significantly prevented the expression of several MMPs and increased type III collagen in the gingiva around the surgical site. Additionally, rutin-treated animals showed enhanced bone formation with higher bone marrow content in the jawbone defect area compared with the control group. Taken together, these findings demonstrate that rutin gel, when added to bone grafts, quickly enhances bone formation and may serve as a suitable alternative to expensive growth factors for the same purpose.