Fungi are a diverse group of organisms that play an essential role in the biosphere. They have a unique ability to produce a vast array of secondary metabolites, including enzymes that have important applications in various industries. Fungal enzymes have been utilized in many fields, such as food processing, textile, paper, and pulp industries, to name a few. In recent years, there has been growing interest in the use of fungal enzymes in the synthesis of pharmaceutical compounds due to their scalability, high catalytic activity, relatively low cost, and ability to catalyze a wide range of chemical reactions under mild reaction conditions making the overall process greener and sustainable. Fungi produce a variety of enzymes such as oxidoreductases, transferases, and hydrolases which can be used in the synthesis of specific compounds with required chemo-, regio-, and stereoselectivity. This paper discusses the role of fungal enzymes in the synthesis of various drugs, active pharmaceutical ingredients (API), and drug intermediates and their applications in the pharmaceutical industry.