For the first time, an endophytic fungus has been isolated from the stems of the medicinal herb Hypericum perforatum (St. John's Wort). The fungus produced the napthodianthrone derivative hypericin ( 1) in rich mycological medium (potato dextrose broth) under shake flask and bench scale fermentation conditions. Emodin ( 2) was also produced simultaneously by the fungus under the same culture conditions. We propose 2 as the main precursor in the microbial metabolic pathway to 1. The fungus was identified by morphology and authenticated by 28S (LSU) rDNA sequencing. Compounds 1 and 2 were identified by LC-HRMS, LC-MS/MS, and LC-HRMS/MS and confirmed by comparison with authentic standards. In bioassays with a panel of laboratory standard pathogenic control strains, including fungi and bacteria, both fungal 1 and 2 possessed antimicrobial activity comparable to authentic standards. This endophytic fungus has significant scientific and industrial potential to meet the pharmaceutical demands for 1 in a cost-effective, easily accessible, and reproducible way.