The marine environment presents a high biodiversity and a valuable source of bioactive compounds with therapeutic and biotechnological potential. Among the organisms present in marine environment, the endophytic fungi isolated from seaweed stand out. These microorganisms have aroused interest in the scientific community regarding its various activities such as antiviral, antimicrobial, antioxidant, photoprotective, cytotoxic, genotoxic, anti-inflammatory, and anticancer, besides establishing important ecological relations with its hosts. Anticancer molecules derived from marine natural sources are a promising target against different types of cancer. The disease’s high rates of morbidity and mortality affect millions of people world wild and the search for new therapeutic alternatives is needed. Thus, this review partially summarizes the methodologies for the isolation of seaweed-derived endophytic fungi, as well as describes the anticancer compounds isolated from such microorganisms, reported in the literature from 2009 to the present. In addition, it describes how some biotechnological processes can help in the discovery of bioactive compounds, especially with anticancer activity.