<p>Vancomycin is widely used for methicillin-resistant <i>Staphylococcus aureus</i> infections. However, it is associated with nephrotoxicity, which is mostly induced by the creation of free radicals in the kidney. Several studies indicated the antioxidant effect of silymarin, particularly nano-formulations with high oral bioavailability. The aim of this study was to evaluate the potential preventive effects of silymarin against vancomycin-induced nephrotoxicity. In this randomized, triple-blinded, placebo-controlled clinical trial, 60 patients who fulfilled the inclusion criteria were randomly assigned to placebo and nano-silymarin (Sinalive® 70 mg twice daily) groups in 1:1 ratio, and received them for a maximum of 14 days beside vancomycin. Patients’ serum creatinine (Scr) and urea and incidence of AKI were assessed on days 3, 7, 10, and 14. The trough level of vancomycin was evaluated 30 min before the fourth dose of vancomycin. AKI incidence was significantly lower in the nano-silymarin group (<i>P</i> &lt; 0.001). The comparison of serum creatinine between the placebo and treatment group showed no significant difference on days 0, 3, 7, and 14; but it was significant on days 10 (<i>P</i> = 0.045). The same finding was found about urea serum levels (<i>P</i> = 0.005 and .016, on days 10 and 14 respectively). Moreover, Scr and urea levels increased considerably in the placebo group during the study (<i>P</i> &lt; 0.001) but not in the silymarin group. Our data suggested that nano-silymarin can be nephroprotective and has a preventive effect against vancomycin nephrotoxicity. However, further human studies are needed to prove these effects. It was registered at the Iranian Registry of Clinical Trials (IRCT20200408046990N9, 2022–04-06).</p>