Acute kidney injury (AKI) is a complex kidney disorder that leads to numerous complications, such as elevated nitrogenous wastes, metabolic acidosis, high potassium levels and even death. The pathogenesis of AKI is very complicated, and its causes are commonly categorized as prerenal, intrinsic or postrenal. In the past few years, evidence has accumulated showing that non-coding RNAs (ncRNAs), such as microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), have significant potential to aid the development of diagnostic and therapeutic strategies of AKI. In this review, we briefly summarize the current understanding of the mechanisms underlying AKI and the main functions of ncRNAs. We mainly focus on revealing the functions of miRNAs (e.g., miR-21, miR-24, miR-30 family, miR-126, miR-127, miR-150, miR-494 and miR-687) and lncRNAs (e.g., TapSAKI, AK139328 and lncRNA-PRINS) in the pathogenesis of AKI.