Background: Cell therapy is applied in tendonitis to speed the healing process of tendon tissue and restore its functional properties. Almost all types of stem cells can differentiate from the recipient cells after transplantation. Objectives: The main goal of this study is to compare the effects of two sources of mesenchymal stem cells on tendon regeneration. Methods: This study randomly divided 32 New Zealand rabbits into 4 groups. The bacterial collagenase was induced at the superficial digital flexor tendon (SDFT) of all rabbits, and the treatment was performed 48 hours after collagenase induction. Group 1 was treated with allogeneic bone marrow mesenchymal stem cells (BMMSCs). Group 2 was treated with adipose-derived stem cells (ADSCs) from the patellar ligament fat pad. Group 3 (sham group) was treated with 0.9% normal saline, and group 4 (control group) was left with no treatment. All rabbits were euthanized 2 and 4 weeks after surgery, and tendon samples were harvested. The histopathology was assessed by hematoxylin-eosin, Masson’s trichrome, and Vangieson’s dye, and tendon structure, fiber arrangement, cell nuclei, tissue inflammation, vascularity (angiogenesis), and density were surveyed. Results: The tendon healing process in the BMMSC and ADSC groups revealed better regeneration than the control and sham groups (P≤0.05). Significant changes (P≤0.05) in some microscopic parameters were seen by comparing the BMMSC and ADSC groups. Conclusion: According to the present study, the injection of mesenchymal stem cells (BMMSCs or ADSCs) showed beneficial results in tendon tissue healing. Furthermore, ADSCs showed better regeneration of the injured tendon tissue than BMMSCs.