Paroxysmal nocturnal hemoglobinuria (PNH), an acquired hematologic disorder characterized by intravascular hemolysis, nocturnal hemoglobinuria, thrombotic events, serious infections, and bone marrow failure, is very rare in children. PNH is caused by a somatic mutation of the phosphatidylinositol glycan (GPI) complementation class A (PIGA) gene, followed by a survival advantage of the PNH clone, which results in a deficiency of GPI-anchored proteins on hematopoietic cells. Currently, immunophenotypic GPI-linked anchor protein analysis has replaced the acid Ham and sucrose lysis test, as it provides a reliable diagnostic tool for this disease. The presence of PNH clones should be considered in every child with an acquired bone marrow failure syndrome, for example (hypoplastic) myelodysplastic syndrome and aplastic anemia, and/or unexpected serious thrombosis. Treatment of PNH in children is dependent on the clinical presentation. In cases of severe bone marrow failure, stem cell transplantation should be seriously considered as a therapeutic option even if no matched sibling donor is available. This article reviews the reported cases of PNH in children using the recently published guidelines for classification, diagnostics, and treatment.