Timor Island is very hot and dry due to the high intensity of sunlight experienced throughout the year. The endophytic fungi Aspergillus flavus had been isolated from medicinal plants such as Catharanthus roseus, Annona squamosa and Curcuma xanthorisa. The endophytic fungi A. flavus from each plant was cultivated on solid rice media and then analyzed for its capability for producing kojic acid. The production of kojic acid was analyzed by HPLC; the highest amount of kojic acid was observed from the endophytic fungi A. flavus, isolated from the stem of Catharanthus roseus, followed by A. flavus from Annona squamosa and Curcuma xanthorisa. Simple VLC fractionation of the extract of A. flavus from C.roseus led to the isolation of around 11.1 g of pure kojic acid. The structure of kojic acid (1) was confirmed by NMR and MS spectroscopic data. A comparison of the NMR data with the literature supported the revision of the natural product flufuran to kojic acid. To the best of our knowledge, this is the first report of a strain of endophytic fungi producing only kojic acid without any other toxic metabolites such as alfatoxins. Therefore, this Aspergillus flavus strain can be applied as a potential producer of kojic acid for industrial use.