Introduction: The establishment of the enthesis unit remains a significant challenge due to the inability to reconstitute the native histological zones postrepair. In this study, the authors investigated the effect of 3-dimensional hyaluronan-based scaffold implanted with Wharton jelly-derived mesenchymal stem cells on enthesis healing in rat model. Methods: Three-dimensional hyaluronan-based scaffold was seeded with mesenchymal stem cells. Bilateral supraspinatus injury model created tendon-bone interface of 48 Sprague-Dawley rats reconstructed with one of the following: group 1: sham surgery; group 2: control group; group 3: surgery, scaffold and conditioned medium; group 4: surgery, scaffold and Wharton jelly-derived mesenchymal stem cells. The rats were killed on day 30, and supraspinatus-humerus tendon to bone unit was harvested en bloc for evaluations. Histopathological, immunohistochemical, mechanical, and micro-computed tomography evaluations were performed. Results: Group 4 was found to be superior to the others in terms of collagen organization and density, fibroblast growth factor, collagen II, and bone morphogenetic protein 2 immunoreactivity, as well as biomechanical tensile strength (P < 0,05). Additionally, groups 3 and 4 exhibited superior bone mineral density and trabecular thickness compared with the other groups. Conclusions: Wharton jelly-derived mesenchymal stem cells implanted into 3-dimensional hyaluronan-based scaffold have shown promising results in achieving a high strength enthesis unit resembling native histological zones.