Introduction and importance: Paroxysmal nocturnal hemoglobinuria (PNH) is a rare disorder caused by a somatic mutation of PIGA (phosphatidylinositol glycan anchor biosynthesis, class A) gene that leads to the destruction of blood cells. Allogeneic haematopoietic stem cell transplant (HSCT) is a treatment option for PHN, but it can cause graft-versus-host disease (GVHD). Long-term immunosuppression as a treatment of GVHD increases the risk for invasive fungal infections such as Case presentation: We present the case of a 22-year-old male with Discussion: The combination of PNH, GVHD, and HSCT created an immunocompromised state, making the patient susceptible to opportunistic infections, including fungal pneumonia. Early recognition of this condition is challenging due to its non-specific symptoms and potential overlap with other post-transplant complications. Timely diagnosis and appropriate treatment, including antifungal therapy and immunosuppression management, are crucial for optimising patient outcomes. Conclusion: This case highlights the importance of early recognition and timely treatment of fungal infections in patients with severe conditions such as GVHD following HSCT for PNH. Timely treatment with appropriate antifungals is necessary for optimal outcomes. Additionally, more research with long-term follow-up and monitoring is necessary to address the necessary knowledge gaps in this field.