Non-coding RNAs (ncRNAs) existing widely in many living organisms are functional RNA molecules, function directly as structural or regulatory RNAs in organisms. Although large and diverse populations of ncRNAs have been extensively studied and well understood in animals and plants, few reports could be found about ncRNAs in fungi. Recently, with the development of modern biological techniques, a number of ncRNAs have been identified in fungi, including snoRNA-derived RNAs, long non-coding RNAs, small interfering RNAs (siRNAs), dsRNA Killer viruses, and novel classes of ncRNAs discovered in filamentous fungi. These ncRNAs play important roles in gene transcription and translation, RNA processing and modifying, chromatin structure, and even fungal pathogenicity. Therefore, studies on ncRNAs in fungi may shed light on the regulatory system of gene expression and the characteristics of fungal growth, and even provide some clues towards understanding pathogenic mechanisms of pathogenic fungi, which will contribute to the treatment of fungal diseases. Here, we reviewed the discovery of fungal ncRNAs, their origins and processing, classification, and biological functions, aiming to establish a theoretical foundation and basis for deep understanding of fungal ncRNAs in future.