In the present study, we investigate and compare the efficacy of bone marrow- and adipose tissue-derived mesenchymal stem cell (MSCs) in corneal wound healing. A penetrating injury was created in the right corneas of Wistar rats (n = 40). Ten microliters of phosphate-buffered solution (PBS) containing 2 × 105 green fluorescent protein (GFP) labeled bone-marrow-derived MSCs to group 1 (n = 15), 10 μl of PBS containing 2 × 105 GFP-labeled adipose-tissue-derived MSCs to group 2 (n = 15), 10 μl PBS was injected into anterior chamber in group 3 (n = 10, control). Corneal opacity scoring, in vivo confocal microscopy, and histopathological evaluation were done at the end of 8 weeks. Immunofluorescence sections were evaluated to detect transplanted cells. Immune staining was performed to measure the expression levels of keratocan, aldehyde dehydrogenase (ALDH) and CD34. The gene expression levels of tumor necrosis factor (TNF-α), the interleukin 6 receptor (IL-6R), interleukin 12b (IL-12b), and transforming growth factor beta (TGF-β1) was measured on corneas. The establishment of stem cells in the corneas of the transplanted groups was confirmed by immunofluorescence staining. The expression of keratocan, ALDH, and CD34 increased in the transplanted groups (p < 0.05). The density of keratocytes increased significantly in both transplanted groups according to the in vivo confocal microscopy data (p < 0.05). The expression of TNF-α, IL-6R, and IL-12b decreased significantly in the transplanted groups (p < 0.05). Based on our findings, we consider that allogeneic stem cells facilitate the regeneration of corneal stroma and can be a cell source for stromal repopulation in diseased cornea.