More than 80% of the Earth surface is consisted of hostile and harsh environments, classified as extreme from an anthropogenic perspective. Microorganisms with acclimatized nature dominate these extreme ecosystems of the biosphere. Survivals in such environments initiate an inductive force leading to the production of noteworthy metabolites having peculiar biochemistry. Recent investigations on extremophilic fungi for unprecedented bioactive compounds emphasize their remarkable potential as sources of new therapeutics. The present review covers the literature published in the last 15 years and highlights the biological activities and structure of compounds isolated from the extremophilic fungi. The compounds are grouped based on their biological functions such as cytotoxicity, lipid-lowering ability, and antimicrobial, antioxidant, nematocidal, anti-inflammatory, anti-malarial, and antifouling activities. A total of 155 compounds isolated from 25 Penicillium species, 16 Aspergillus species, and 23 other species are presented, which include 105 new and 50 known bioactive compounds. Out of these, 77 have known cytotoxic activity and 46 are antimicrobial in nature, while there are 32 other compounds with different activities including nematocidal, anti-allergic, antioxidant, and anti-inflammatory. KEY POINTS: • A broad compilation of bioactive compounds from extremophilic fungi. • Classification of bioactive compounds based on their biological functions. • Production of cytotoxic compounds is common among all kind of extremophilic fungi. • Bioactive compounds have no direct role in adaptation process of extremophiles.