Agave sisalana, known as sisal, yields the world’s main natural stiff fiber used to produce various industrial products. The Brazilian semiarid is the largest sisal producing region in the world; however, production is under threat by sisal bole rot disease, caused by Aspergillus welwitschiae. Since chemical control of this disease is questionable in drought-ridden areas with little investment in crop management and due to environmental and public health concerns, the search for a biocontrol agent against A. welwitschiae is warranted. In this work, we isolated and identificated Penicillium citrinum as an endophyte from sisal plants collected from the Brazilian semi-arid and investigated whether it could be a biocontrol agent against sisal bole rot. P. citrinum inhibited the mycelium growth of A. welwitschiae by 65.8% when inoculated 72 hours before the pathogen, in dual culture medium assays. We found that P. citrinum can reduce sisal bole rot disease up to 90% when inoculated in sisal plants 48 hours before pathogen inoculation. Altogether, our data suggest a potential role for P. citrinum in the control of sisal bole rot disease.