Endophytic fungi are potential sources of bioactive secondary metabolites that can be exploited for therapeutic purposes. Our study was aimed to identify bioactive secondary metabolites from crude extracts of endophytic fungi of three popular medicinal plants (Alstonia boonei- Ahun, Enantia chlorantha- Awopa and Kigelia africana- Pandoro) that have ethnobotanical history in Nigeria. The endophytic fungi were isolated from the stem barks of the plants using standard procedures. They were later fermented in broth culture, and the extract from the cell free broth of each of the fungi was subjected to Gas-Chromatography Mass-Spectrophotometry (GCMS). The results showed that, twenty-one different compounds were characterised from Aspergillus niger, Macrophomina sp, Trichoderma sp. and Penicillium species. The bioactive compounds include; Griseofulvin, Cinnamic acids, Penicillin, Coumarin, Cubenol, Erythritol among others. The presence of these compounds may contribute to the therapeutic properties of the plants.