Acute kidney injury (AKI) is a serious threat for human health and life. High dose of vancomycin (VAN) can give rise to AKI. The roles and molecular basis of long noncoding RNA plasmacytoma variant translocation 1 (PVT1) in VAN-induced AKI have been poorly defined till now. Protein levels of p65, phosphorylated p65 (p-p65), NF-κB inhibitor alpha (IκBα), phosphorylated IκBα (p-IκBα), Bcl-2 and Bax were measured by western blot assay. RNA levels of PVT1 and microRNA-124 (miR-124) were determined by RT-qPCR assay. HK-2 cell apoptosis was detected by an Annexin V-FITC apoptosis detection assay. Kidney functions were assessed by blood urea nitrogen (BUN) level, serum creatinine (Scr) level, histopathologic analysis, and TUNEL assay. Bioinformatical analysis, luciferase reporter assay, RIP and RNA pull down assays were performed to explore whether PVT1 could interact with miR-124. PVT1 was highly expressed in VAN-induced AKI models. Functional analysis revealed that PVT1 knockdown ameliorated VAN-induced AKI in vivo. Further exploration manifested that PVT1 directly interacted with miR-124. Moreover, the silencing of PVT1 abated VAN-induced HK-2 cell apoptosis in vitro, while this effect was reversed by the miR-124 inhibitor. Also, VAN treatment resulted in the reduction of miR-124 expression and the activation of NF-κB signaling in HK-2 cells. The inhibition of NF-κB alleviated VAN-induced HK-2 cell apoptosis. PVT1 activated NF-κB signaling by targeting miR-124 in VAN-induced HK-2 cells. PVT1 knockdown lessened VAN-induced AKI by targeting miR-124 via inactivating the NF-κB signaling, elucidating the critical roles and molecular basis of PVT1 in VAN-induced AKI and highlighting the diagnostic and therapeutic values of PVT1 in AKI.