Paroxysmal nocturnal hemoglobinuria (PNH) in childhood occasionally develops into aplastic anemia (AA) during the progression of the disease (AA-PNH syndrome). Here, a case of a 12-year-old female AA patient treated with immunosuppressive therapies is presented. She developed PNH but was asymptomatic other than hemolysis for 8 years. Because she experienced thrombosis with severe abdominal symptoms, eculizumab was initiated at 20 years of age. After the treatment, her hemolysis and symptoms of thrombosis were dramatically improved. Subsequent medication switching from eculizumab to ravulizumab led to a prolongation of the period between hospital visits and high quality of life. In childhood-onset AA, it is very important to prevent the development of the pathological condition over a long period of time and to choose treatments suitable for the patient’s life stages.