Flavonoids have a broad spectrum of established positive effects on human and animal health. They find an application in medicine for disease therapy and chemoprevention, whence the interest in flavonoids increases. In addition, they are used in food and cosmetic industries as pigments and biopreservatives. Plants are an inexhaustible source of flavonoids. The most important step of plant raw material processing is extraction and isolation of target compounds. The quality of an extract and efficiency of a procedure are influenced by several factors: Plant material and pre-extracting sample preparation, type of solvent, extraction technique, physicochemical conditions, etc. The present overview discusses the common problems and key challenges of the extraction procedures and the different mechanisms for selective extraction of flavonoids from different plant sources. In summary, there is no universal extraction method and each optimized procedure is individual for the respective plants. For an extraction technique to be selective, it must combine an optimal solvent or mixture of solvents with an appropriate technique. Last but not least, its optimization is important for a variety of applications. Moreover, when the selected method needs to be standardized, it must achieve acceptable degree of repeatability and reproducibility.