(1) Background: The current treatment for osteoarthritis is ineffective due to its focus on pain relief and lack of cartilage repair. Viscosupplementation such as hyaluronic acid improves symptoms but remains unnoticed for several months. Researchers are exploring cell-based therapies such as mesenchymal stem cells secretome and mesenchymal stem cells, which can repair cartilage damage. The objective of the research is to evaluate and compare the effectiveness of the secretome derived from umbilical cord mesenchymal stem cells (UC-MSCs) with hyaluronic acid (HA). (2) Methods: An open-label clinical trial involving 30 knee osteoarthritis patients divided into two groups received UC-MSC secretome and hyaluronic acid doses. The study assessed clinical outcomes using VAS and WOMAC and measured MMP-3 and TGF-β1 levels before and after treatment. (3) Results: A study of 30 subjects found that the UC-MSC secretome group showed a decrease in pain in the OA knee compared to the HA group. The therapy was most effective after the third injection, and the group showed a decrease in the MMP-3 ratio and an increase in TGF-β1 compared to the hyaluronic acid group. (4) Conclusions: UC-MSC secretome intra-articular injections showed superior clinical improvement, biomarker changes, and no side effects compared to hyaluronic acid over a 5-week interval.