Fungi represent a diverse class of microorganisms with promising applications in vast areas. Fungi are considered a rich source of thousands of secondary metabolites with potential therapeutic properties. Besides other applications of secondary metabolites, their role in the discovery and development of drugs remains of utmost importance. Fungal secondary metabolites (SMs) have various biological properties and variations in chemical and biological properties, thus becoming an important lead substance to be used as drug molecules. Currently, a good number of drug candidates are identified from fungal sources. The advantages of using fungal metabolites as lead drug candidates include easy production, low cost, greater bioactivity, and greater availability. Advances in genomics also added to the identification of fungal secondary metabolites as drug precursor molecules and thus enhanced the accuracy, lowered the screening time, and elucidated the drug-related properties at the genetic level. Nevertheless, fungal metabolites have greater drug-like properties, but still, challenges and limitations exist. For instance, antibiotic resistance, difficulty in fungal growth, and extensive clinical trials can limit the potential of fungal SMs as drugs. While intellectual property rights, patenting, and lengthy approval process can limit their commercialization. In the future, the usage of advanced technologies, computational tools, and artificial intelligence tools can overcome these limitations and will add more to the fungal secondary metabolites drug properties.