Purpose: This study aimed to evaluate the effect of intraoperative mesenchymal stem cell injection on healing outcome in secondary cleft lip correction. Patients and Methods: A total of ten patients with secondary cleft lip deformities who needed secondary cleft lip repair were included in this study. The patients were divided equally into two groups: group I (study group) were subjected to secondary cleft lip repair with immediate intraoperative bone marrow mesenchymal stem cells injection (BM-MSCs), group Ⅱ (control group) who didn't receive any type of injection neither during surgery nor after. The healing out come and scar progression were recorded through photographs and Ultrasonography (US). Results: Group I showed higher rate in primary healing outcome than that of group Ⅱ. The Ultrasound revealed statistically significant difference in scar progression in both groups. Group I showed statistically significant difference in scar measurements across time than group Ⅱ in p < 0.01. Conclusion: Bone marrow mesenchymal stem cell injection in cleft lip correction has a good effect on primary healing outcome and scar progression.