Paroxysmal nocturnal hemoglobinuria (PNH) is a rare clonal blood disorder that presents chronic intravascular hemolysis. PNH concomitant with inherited hemolytic anemia has been rarely reported. Here, we report an interesting PNH patient who was misdiagnosed with iron deficiency anemia due to concomitant heterozygous β-thalassemia. The patient experienced dizziness, fatigue, and restricted physical activity for the previous 3 years. Thalassemia gene analysis revealed heterozygous β-thalassemia. Iron staining of the bone marrow demonstrated the absence of stainable iron and sideroblasts. The patient was diagnosed with iron deficiency anemia. Iron supplementation treatment was performed, but the anemia remained unresolved. The patient became transfusion dependent 1 year later and was admitted to our hospital in March 2010. Flow cytometry of the patient's peripheral blood demonstrated that 7.9% and 11.9% of the erythrocytes were CD59 and CD55 deficient, respectively. The patient was finally diagnosed with concomitant PNH and heterozygous β-thalassemia.