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Objective: Knee Osteoarthritis (KOA) is a debilitating degenerative joint ailment afflicting millions of patients. Numerous studies have assessed the efficacy of mesenchymal stem cells (MSCs) derived from various sources for KOA treatment, yet direct comparisons are scarce and inconsistent. Furthermore, network meta-analysis (NMA) conclusions require updating, while the safety of MSCs therapy remains contentious. This study evaluates therapeutic approaches involving MSCs from different sources in patients with KOA through randomized controlled trials (RCTs) and cohort studies. The objective is to compare the effectiveness and safety of MSCs strategies from various sources for KOA treatment. Methods: A systematic literature review was conducted to identify RCTs and cohort studies comparing different sources of MSCs in KOA patients. A randomized effects network meta-analysis was used to concurrently evaluate both direct and indirect comparisons across all protocols. Results: The NMA included 16 RCTS and reported 1005 participants. Adipose-derived mesenchymal stem cells (AD-MSCs) were the most effective treatment, showing significant improvements in the Visual Analogue Scale (VAS), the Short Form 36 (SF-36 scale), the International Knee Literature Committee Knee Evaluation Scale (IKDC subjective scores), and the Knee Injury and OA Outcome Score (KOOS). The probabilities are P = 85.3, P = 70.5, P = 88 and P = 87, respectively. Compared with placebo, AD-MSCs resulted in a VAS Score (SMD 0.97; 95%CI 0.37, 1.57), IKDC subjective scores (SMD −0.71; 95%CI −1.20, −0.21) was significantly reduced. Umbilical cord-derived mesenchymal stem cells (UC-MSCs) showed significant improvements in the University of Western Ontario and McMaster University OA (WOMAC) (P = 91.4). Compared with placebo, UC-MSCs had a higher WOMAC Score (SMD 1.65; 95%CI 0.27, 3.03) and ranked first. Compared with MSCs, placebo emerged as the safer option (P = 74.9), with a notable reduction in AEs associated with HA treatment (RR 0.77; 95%CI 0.61, 0.97). AD-MSCs were found to have the least favorable impact on AEs with a probability of P = 13.3. Conclusions: This network meta-analysis established that MSCs offer pain relief and enhance various knee scores in KOA patients compared to conventional treatment. It also identifies other therapeutic avenues warranting further exploration through high-quality studies. Nonetheless, it underscores the necessity to emphasize the potential complications and safety concerns associated with MSCs.