Invasive candidiasis remains an important cause of mortality and morbidity in patients with underlying diseases. Here, we report a case of gastric perforation due to Candia glabrata infection in a 74-year-old-male with Paroxysmal nocturnal hemoglobinuria (PNH) who received long-term corticosteroid treatment of hemophagocytic syndrome associated with acute cholecystitis. Total gastrectomy was performed, and he was treated liposomal amphotericin B. The patient was extubated successfully on the 2nd postoperative day, but the patient died of Pneumocystis jirovecii pneumonia (PJP). An autopsy revealed that there was a small amount of the cystic form of Pneumocystic jirovecii, but there was not the presence of Candida spp. Concerning the prophylaxis of invasive candidiasis, there is no strong evidence-based data in clinical practice in immunocompromised patients, such as those receiving long-term immunomodulatory therapy or corticosteroids. Our present case suggests the importance of fungal management and may indicate the need for a new approach to the fungal prophylaxis in such patients.