Scedosporium apiospermum is an opportunistic fungus in humans. The incidence of S. apiospermum infection in patients with acquired neutropenia (e.g., patients receiving chemotherapy and bone marrow transplant recipients) is steadily increasing. S. apiospermum has poor in vitro susceptibility to “conventional” antifungal agents, rendering the management of infections complex. Patients with chronic granulomatous disease (CGD) are highly susceptible to fungal infections, which are mostly due to Aspergillus species. We describe two children with CGD and invasive pulmonary infection due to S. apiospermum. Both patients were treated with antifungal therapy including azole derivatives (itraconazole or voriconazole) and surgical resection of infected tissues. These cases highlight that scedosporium infection can closely mimic aspergillus infection and should be considered in any case in which there is a failure to respond to appropriate “conventional” antifungal therapy. We also suggest that the emergence of this pathogen may have been favored by long-term use of amphotericin B in both patients.