Endophytes, a potential source of bioactive secondary metabolites, were isolated from the widely used medicinal plant Calotropis procera Ait. Approximately 675 segments from 15 Calotropis procera plants and 15 latex samples were assessed for the presence of endophytic fungi. Finally, eight fungal species were isolated and identified based on their macro- and micro-morphology. The endophytic fungal filtrates were screened for their antimicrobial activity against 11 important pathogenic micro-organisms. The filtrates of nanoparticles were from three of the eight isolated endophytic fungi, namely, Penicillium chrysogenum, Aspergillus fumigatus and Aspergillus flavus, and were highly effective against the tested bacteria, while the remaining endophytic fungal filtrates displayed low activity.