Epigenetic modifications are increasingly recognized to play a significant contribution in diabetic nephropathy (DN). Histone deacetylases (HDACs) are the emerging target in the pathogenesis and progression of DN. Valproic acid (VPA), a widely used anti-epileptic drug and has been proven as an HDAC inhibitor. This study was aimed to evaluate the protective roles of VPA on HDAC-mediated NF-κB/iNOS signaling and autophagy in DN. Diabetes was induced by a single injection of STZ (50 mg/kg), whereas VPA at the doses of 150 and 300 mg/kg/day for 8 weeks was administered by oral route in Sprague-Dawley rat. Blood and urine were collected before animal were sacrificed, while kidneys were dissected after sacrificed. The podocyte and renal injuries were assessed using biochemical markers, histology, podocyte effacement, DNA damage and apoptosis as well as protein expression evaluation. VPA treatment improves the plasma and urinary biomarkers of renal function, decreased expression of iNOS, 3-nitrotyrosine, NF-κB, p-NF-κB, HDAC4/5, calmodulin, calbindin, apoptosis and DNA damage. Further, VPA treatment increased histone acetylation and ameliorated the histological alterations and podocyte effacement. Interestingly, VPA treatment also restored diabetes-associated perturbations in autophagy by HDAC inhibition. To the best of our knowledge, this is the first report, which highlights the beneficial role of VPA in DN. The present results clearly exhibited that VPA treatment ameliorates the podocyte and renal injuries mainly by facilitating the autophagy and inactivation of NF-κB/iNOS signaling. The present findings demonstrated that VPA may be useful in the treatment of DN, since the present experimental doses are clinically relevant.