Valproic acid (VPA) is a histone deacetylase inhibitor that is used mainly as an antiepileptic and anticonvulsant drug. The side effects of VPA usually appears as hepatic injury and various metabolic disorders. On the other hand, it is rarely reported to cause kidney injury. Despite the many studies on the influence of VPA exposure on the kidneys, the specific mechanism remains unclear. This study examined the changes after VPA treatment to the mouse kidney stem cells (mKSCs). VPA triggers an increase in mitochondrial ROS, but there was no change in either mitochondrial membrane potential or the mitochondrial DNA copy number in mKSCs. The VPA treatment increased the mitochondrial complex III but decreased complex V significantly compared to the DMSO treatment as a control. The inflammatory marker (IL-6) and the expression of the apoptosis markers (Caspase 3) and were increased by VPA. In particular, the expression of the podocyte injury markers (CD2AP) was increased significantly. In conclusion, VPA exposure has adverse effects on mouse kidney stem cells.