Advanced transcriptomic technology has identified a great number of non-coding RNAs (ncRNAs) that are pervasively transcribed in the yeast genome. ncRNAs can be classified into short ncRNAs (<200 nt) and long ncRNAs (lncRNAs; >200 nt). Those transcripts are strictly regulated through transcription and degradation mechanisms to maintain proper cellular homeostasis and prevent aberrant expression. It has been revealed that ncRNAs can play roles in various regulatory processes, particularly in transcriptional regulation. While short ncRNAs are well characterised, the function of lncRNAs remains poorly understood. Both functional and transcriptional profiling have been applied to fill the gap in the lncRNA functions landscape. It has been proven by functional profiling that these long transcripts can serve important cellular roles in gene regulation, RNA metabolism, sexual differentiation and telomeric overhang homeostasis. In addition, transcriptional profiling allowed the characterisation of ncRNAs involved in the cell cycle, colony subpopulation dynamics, virulence and regulatory networks. In this review, we introduce the classification, the cellular fate, the evolution and conservation, the mechanisms of action, and the profiling of yeast ncRNAs.