Paroxysmal nocturnal hemoglobinuria (PNH) is a rare disorder associated with an acquired clonal defect of the hematopoietic stem cell. Abnormal expression of complement inhibitors results in hemolysis and thromboembolic complications. Here we present two pediatric cases of PNH. The first patient died due to progressive and nonspecific thromboembolic complications, particularly affecting the abdominal organs and vessels. Allogeneic bone marrow transplantation from a related donor, liver transplantation, and complement inhibitor therapy were not feasible. In the second patient, treatment with hematopoietic stem cell transplantation from an unrelated donor was successful, although complicated by episodes of graft-versus-host disease (GvHD) and recurrent viral infections. Considering the specific nature of PNH, early diagnosis and careful management of complications during treatment remain essential aspects.