The aim was to evaluate the effects of mesenchymal stem cell (MSC) transfer to periodontal ligament (PDL) on the inhibition and/or repair of orthodontically induced root resorption (OIRR) during and after arch expansion and on the orthodontic tooth movement (OTM) rate of the maxillary first molar teeth of rats. Sixty Wistar rats were divided into three groups as the untreated group, MSC and control injections during the expansion period group (EMSC-EC), and MSC and control injections at the retention period group (RMSC-RC). Fifty grams of orthodontic force was applied to the maxillary first molar teeth of the rats for 14 days in the vestibular direction, and then, 20 days of retention was carried out. MSCs and control injections were performed every 3 days in the EC, RC, EMSC, and RMSC groups. At the end of the experiment, samples were prepared for OTM evaluation, mRNA expression analysis, micro-computed tomography measurements, cementum thickness calculations, and structural examinations. The amount of OTM in EMSC group was significantly higher than in EC group (P < 0.001). MSC transfer during the expansion and retention periods reduced the number of resorption lacunae, volumetric and linear resorptive measurements, and cyclooxygenase-2 and receptor activator of nuclear factor kappa B ligand (RANKL) mRNA expression levels, and increased the osteoprotegerin (OPG) expression levels, OPG/RANKL ratio, and cementum thickness in the EMSC and RMSC groups. MSC transfer to PDL during expansion increased the amount of OTM. Injection of MSC during the retention period was found to be slightly more effective in prevention and/or repair of OIRR than MSC transfer during the expansion period.