Background: In the oral cavity, the potential application of stem cell therapy has been implied in different conditions including periodontal disease. The increased incidence rate of periodontitis, especially in developing countries, with lack of novel treatment modalities introduced that can help speed-up the healing process can imply the need for new approaches such as using stem cells. Aim of the study: To histologically evaluate the effect of mesenchymal stem cell therapy on the healing of periodontal fibers, in albino rats suffering from periodontal disease. Material and Methods: Periodontitis was induced in a total number of 36 albino rats, divided into 4 groups evenly. 2 control group, and 2 study groups based on the date of sacrifice (2 and 6 weeks). Evaluation of the periodontal condition was performed using ordinary Hematoxylin and eosin staining, Masson's trichrome special stain, and β-catenin immunohistochemical staining to evaluate number of proliferating periodontal fibroblasts. To investigate the effects of the use of stem cells, time, and their interactions on the mean cell count, two-way ANOVA was conducted. If the ANOVA test revealed a significant outcome, Bonferroni post-hoc correction was used to identify which specific groups differed from each other. Results: Highest area percentage of Masson's trichrome stain, and β-catenin immuno-positive cell count was found in the group treated with stem cells for 6 weeks. Conclusion: Stem cells administration improved collagen quality and encouraged proliferation of periodontal cells in a time-dependent manner, when compared to groups not treated with stem cells.