A normal karyotype is usually present in cases of classic paroxysmal nocturnal hemoglobinuria (PNH), whereas chromosomal abnormalities involving chromosome bands 13q12 to 13q14 (13q12q14) are frequently found in various hematologic malignancies, including chronic lymphoblastic leukemia (CLL) and myelodysplastic syndrome (MDS). Here, we present a case of a 55-year-old male patient with PNH who had a deletion of chromosome 13q [del(13q)]. He presented with cough, fever, and pancytopenia. Flow cytometry of the patient's peripheral blood demonstrated that 21.7% and 21.5% of the erythrocytes were CD59 and CD55 deficient, respectively, and 63.5% of the granulocytes were FLAER and CD24 deficient. Examination of the bone marrow indicated that blasts were not increased but mild dyshematopoietic features were present. Conventional cytogenetic analysis and fluorescence in situ hybridization revealed a deletion of chromosome 13q (q12q14). The patient received an allogeneic hematopoietic stem cell transplantation. Whether this abnormality can be considered as an evidence of MDS in the setting of overt PNH requires an evaluation in the future.