Endophytes have continued to gain fame due to their ability to produce an array of secondary metabolites within the host system with huge untapped pharmacological potentials. This study was carried out to further identify and isolate novel therapeutic compounds from Fusarium equiseti, an Endophytic fungus isolated from leaves of Ocimum gratissimum. Endophytic fungal isolation, fungal fermentation, and extraction of secondary metabolites were carried out using standard laboratory methods. The crude extracts of Fusarium equiseti were subjected to further chromatographic techniques using vacuum liquid chromatography, Sephadex LH 20 and semipreparative HPLC for isolation of bioactive compounds. The fractions and the isolated compounds obtained were further subjected to high performance liquid chromatography-Diode Array Detector (HPLC-DAD). The analytical HPLC led to the further detection of many bioactive compounds namely: Enniatin A, Aureonitol, Serasinoside H1, Altenusin, Aplysinamisin, benzylnitril, ruspolinone and Orientin. Semipreparative HPLC led to the isolation of 6 pure compounds of which two were identified as benzylnitril, and ruspolinone. The remaining four were not identified due to lack of library hits. The detected and the isolated compounds have been previously shown to exhibit a wide array of biological activities including antiviral, antifungal, hepatoprotection, antibacterial, anticancer, cytotoxic, and antioxidant properties. The unidentified compounds may hold enormous potential as new bioactive lead compounds for development into novel therapeutic agents. Therefore, the Endophytic fungus, Fusarium equiseti should be harnessed for its potential pharmacological, pharmaceutical, agricultural and industrial applications.