Medicinal mushrooms are higher fungi that consist of ascomycetes, basidiomycetes, and imperfect fungi. They have been long used as tonic and traditional medicine in East Asia, Europe, and Africa. Contemporary pharmacological researches have revealed that they possess a wide spectrum of bioactivity due to their production of a variety of bioactive compounds. Some of them have entered into the market; some are ready for industrial trials and further commercialization, while others are in various stages of development. According to the purpose of usage, a variety of medicinal mushroom-based products have been developed, which could be roughly divided into three general categories, i.e., nutraceuticals/functional foods, nutriceuticals/dietary supplements, and pharmaceuticals. Accordingly, the downstream processing of medicinal mushroom products varies greatly. Indeed, a major characteristic of medicinal mushroom is the wide variety of secondary metabolites, due to which a broad spectrum of separation techniques must be employed. In this chapter we will present an overview of the achievements in downstream processing technology for medicinal mushroom products. Examples of separation of products such as bioactive high-molecular-weight products like polysaccharides and low-molecular-weight products like triterpenoids are given. The application of some special separation strategy, e.g., chemical reaction-assisted separation for tackling some analogs with similar physicochemical properties from medicinal mushroom, is also described.