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Endophytes either be bacteria, fungi, or actinomycetes colonize inside the tissue of host plants without showing any immediate negative effects on them. Among numerous natural alternative sources, fungal endophytes produce a wide range of structurally diverse bioactive metabolites including anticancer compounds. Considering the production of bioactive compounds in low quantity, genetic and physicochemical modification of the fungal endophytes is performed for the enhanced production of bioactive compounds. Presently, for the treatment of cancer, chemotherapy is majorly used, but the side effects of chemotherapy are of prime concern in clinical practices. Also, the drug-resistant properties of carcinoma cells, lack of cancer cells-specific medicine, and the side effects of drugs are the biggest obstacles in cancer treatment. The interminable requirement of potential drugs has encouraged researchers to seek alternatives to find novel bioactive compounds, and fungal endophytes seem to be a probable target for the discovery of anticancer drugs. The present review focuses a comprehensive literature on the major fungal endophyte-derived bioactive compounds which are presently been used for the management of cancer, biotic factors influencing the production of bioactive compounds and about the challenges in the field of fungal endophyte research.