Chronic kidney disease (CKD) is caused by dysfunctional kidneys, which result in complications like cardiovascular diseases. CKD-induced pathophysiological conditions decrease efficacy of autologous mesenchymal stem/stromal cell (MSC)-based therapy by reducing MSC functionality. To enhance therapeutic potential in patients with CKD, we isolated exosomes derived from melatonin-treated healthy MSCs (MT-exosomes) and assessed the biological functions of MT-exosome-treated MSCs isolated from patients with CKD (CKD-MSCs). Treatment with melatonin increased the expression of cellular prion protein (PrP ) in exosomes isolated from MSCs through the upregulation of miR-4516. Treatment with MT-exosomes protected mitochondrial function, cellular senescence, and proliferative potential of CKD-MSCs. MT-exosomes significantly increased the level of angiogenesis-associated proteins in CKD-MSCs. In a murine hindlimb ischemia model with CKD, MT-exosome-treated CKD-MSCs improved functional recovery and vessel repair. These findings elucidate the regenerative potential of MT-exosome-treated CKD-MSCs via the miR-4516-PrP signaling axis. This study suggests that the treatment of CKD-MSCs with MT-exosomes might be a powerful strategy for developing autologous MSC-based therapeutics for patients with CKD. Furthermore, miR-4516 and PrP could be key molecules for enhancing the regenerative potential of MSCs in ischemic diseases.